Table of Contents

Edward C. Grady		James F. Gentilcore
President and Chief Executive Officer		President and Chief Executive Officer
Brooks Automation, Inc.		Helix Technology Corporation

---

Table of Contents

	•	a prospectus of Brooks under Section 5 of the Securities Act of 1933, as amended, and the rules thereunder, which is referred to in this joint proxy statement/ prospectus as the Securities Act, with respect to the shares of Brooks common stock to be issued to the holders of Helix common stock in the merger;
	•	a proxy statement of Brooks and of Helix under Section 14(a) of the Securities Exchange Act of 1934, as amended, and the rules thereunder, which is referred to in this joint proxy statement/ prospectus as the Exchange Act; and
	•	a notice of special meeting with respect to the Brooks special meeting of stockholders and the Helix special meeting of stockholders, at which, among other things, the stockholders of each company will consider and vote upon the Brooks proposal to approve the issuance of shares of Brooks common stock in the merger and the Helix proposal to adopt the merger agreement, as amended, as the case may be.

---

Table of Contents

	1. To approve the issuance of shares of Brooks common stock pursuant to the Agreement and Plan of Merger, dated as of July 11, 2005, among Brooks, Mt. Hood Corporation, which is referred to in this joint proxy statement/ prospectus as Mt. Hood, and Helix, as amended on August 29, 2005, a copy of which is attached as Annex A to this joint proxy statement/ prospectus;
	2. To approve a proposal to amend Brooks’ certificate of incorporation if the merger is consummated to increase Brooks’ authorized shares of common stock from 100,000,000 shares to 125,000,000 shares;
	3. To permit Brooks’ board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve either of the foregoing proposals; and
	4. To act upon such other matters as may properly come before the special meeting or any adjournments or postponements thereof.

	By Order of the Board of Directors
	Thomas S. Grilk
	Senior Vice President,
	General Counsel and Secretary

---

Table of Contents

	1. To adopt the Agreement and Plan of Merger, dated as of July 11, 2005, among Brooks, Mt. Hood and Helix, as amended on August 29, 2005, a copy of which is attached as Annex A to this joint proxy statement/ prospectus;
	2. To permit Helix’s board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve the Helix merger proposal; and
	3. To act upon such other matters as may properly come before the special meeting or any adjournments or postponements thereof.

	By Order of the Board of Directors
	Beverly L. Couturier
	Corporate Secretary

---

Table of Contents

QUESTIONS AND ANSWERS ABOUT THE MERGER				iv
SUMMARY				1
	Information about Brooks			1
	Information about Helix			1
	Information about Mt. Hood			1
	Risk Factors			2
	The Brooks Special Meeting			3
	The Helix Special Meeting			3
	The Merger			4
	Recommendation of Brooks’ Board of Directors; Brooks’ Reasons for the Merger			5
	Recommendation of Helix’s Board of Directors; Helix’s Reasons for the Merger			5
	Opinion of Brooks’ Financial Advisor			6
	Opinion of Helix’s Financial Advisor			6
	Share Ownership of Directors and Executive Officers of Brooks and Helix			6
	Interests of Helix’s Directors and Executive Officers in the Merger			6
	Board of Directors and Executive Officers of the Surviving Corporation			7
	Conditions to Completion of the Merger			7
	Termination of the Merger Agreement			7
	Termination Fees and Expenses			8
	No Solicitation			9
	Regulatory Matters			9
	Material U.S. Federal Income Tax Consequences			9
	Accounting Treatment			9
	Comparison of Rights of Stockholders			9
	No Appraisal Rights			9
	Selected Consolidated Historical Financial Data of Brooks			10
	Selected Consolidated Historical Financial Data of Helix			12
	Summary Unaudited Pro Forma Condensed Combined Financial Data			13
	Financial Summary			14
	Comparative Per Share Information			16
	Comparative Market Value Information			17
RISK FACTORS				18
CAUTIONARY STATEMENT CONCERNING FORWARD-LOOKING STATEMENTS				24
THE BROOKS SPECIAL MEETING				25
	Joint Proxy Statement/ Prospectus			25
	Date, Time and Place of the Special Meeting			25
	Purpose of the Special Meeting			25
	Stockholder Record Date for the Special Meeting			25
	Quorum; Vote Required for Each Proposal			26
	Adjournment or Postponement			26
	Proxies			26
	Solicitation of Proxies			27
THE HELIX SPECIAL MEETING				28
	Joint Proxy Statement/ Prospectus			28
	Date, Time and Place of the Special Meeting			28
	Purpose of the Special Meeting			28
	Stockholder Record Date for the Special Meeting			28

---

Table of Contents

	Quorum; Vote Required for Each Proposal			28
	Adjournment or Postponement			29
	Proxies			29
	Solicitation of Proxies			30
PROPOSAL NUMBER ONE: THE MERGER PROPOSALS				31
	Background of the Merger			31
	Recommendation of Brooks’ Board of Directors; Brooks’ Reasons for the Merger			40
	Recommendation of Helix’s Board of Directors; Helix’s Reasons for the Merger			42
	Opinion of Brooks’ Financial Advisor			45
	Opinion of Helix’s Financial Advisor			53
	Interests of Helix’s Directors and Executive Officers in the Merger			59
	Consummation and Effectiveness of the Merger			62
	Conversion of Helix Common Stock			62
	Treatment of Helix Stock Options			62
	Regulatory Matters			62
	Delisting and Deregistration of Helix Common Stock			63
	Accounting Treatment			63
	No Appraisal Rights			63
	Federal Securities Laws Consequences; Resale Restrictions			63
MATERIAL U.S. FEDERAL INCOME TAX CONSEQUENCES				64
	Material U.S. Federal Income Tax Consequences of the Merger			64
	Tax Opinions as Condition to Merger			66
	Backup Withholding			66
	Net Operating Loss Carryforwards of Brooks			66
THE MERGER AGREEMENT				67
	General			67
	The Merger; Certificate of Merger			67
	Merger Consideration			67
	Exchange of Shares			68
	Representations and Warranties			69
	Covenants and Agreements			70
	Officers and Directors of Brooks After the Effective Time			73
	Officer and Director Indemnification and Insurance			73
	Conditions Precedent			74
	No Solicitation			75
	Change of Recommendation			76
	Termination of the Merger Agreement			77
	Termination Fees and Expenses			79
	Amendment and Waiver			79
	Governing Law			80
BOARD OF DIRECTORS AND MANAGEMENT OF BROOKS FOLLOWING THE MERGER				81
BROOKS BENEFICIAL OWNERSHIP				84
HELIX BENEFICIAL OWNERSHIP				86
INFORMATION ABOUT BROOKS				88
INFORMATION ABOUT HELIX				89
UNAUDITED PRO FORMA CONDENSED COMBINED FINANCIAL INFORMATION				90

ii

---

Table of Contents

DESCRIPTION OF BROOKS CAPITAL STOCK				100
	Authorized Capital Stock			100
	Brooks Common Stock			100
	Options			101
	Rights Agreement			101
	Anti-Takeover Effects of Provisions of Brooks’ Certificate of Incorporation, Bylaws, Stockholder Rights Plan, Indenture and Delaware Law			101
COMPARISON OF RIGHTS OF STOCKHOLDERS				103
BROOKS STOCKHOLDERS ONLY — BROOKS PROPOSAL NUMBER TWO:
	AMENDMENT TO BROOKS’ CERTIFICATE OF INCORPORATION			108
	Purpose and Effect of Amendment to Brooks’ Certificate of Incorporation			108
	Vote Required			109
	Recommendation of the Board of Directors			109
BROOKS STOCKHOLDERS ONLY — BROOKS PROPOSAL NUMBER THREE:
	POSSIBLE ADJOURNMENT OF THE BROOKS SPECIAL MEETING			110
HELIX STOCKHOLDERS ONLY — HELIX PROPOSAL NUMBER TWO:
	POSSIBLE ADJOURNMENT OF THE HELIX SPECIAL MEETING			111
LEGAL MATTERS				112
EXPERTS				112
SUBMISSION OF FUTURE STOCKHOLDER PROPOSALS				113
HOUSEHOLDING OF PROXY MATERIALS				114
WHERE YOU CAN FIND MORE INFORMATION				115
	Brooks SEC Filings			115
	Helix SEC Filings			116
Annex A: Agreement and Plan of Merger, as amended				A-1
Annex B: Opinion of Needham & Company, LLC				B-1
Annex C: Opinion of Morgan Stanley & Co. Incorporated				C-1

iii

---

Table of Contents

Q:		What will happen in the merger?
A:		We are proposing to combine our companies in a “merger” transaction. In the transaction, Mt. Hood, a Delaware corporation and newly formed, wholly owned subsidiary of Brooks, will merge with and into Helix. As a result of this merger, Helix will become a wholly owned subsidiary of Brooks. The merger agreement contemplates, but does not require, that Helix will be merged with and into Brooks following the merger of Mt. Hood with and into Helix. This subsequent merger, if it occurs, would be undertaken to simplify the organizational structure of Brooks following the combination and would have no impact on the holders of Brooks or Helix common stock.
Q:		What will I receive in the merger?
A:		If the merger is consummated, Helix stockholders will receive 1.11 shares of Brooks common stock for each share of Helix common stock that they own. Helix stockholders will also receive a cash payment for any fractional shares. For example, a Helix stockholder who holds 99 shares of Helix common stock will receive 109 shares of Brooks common stock (99 multiplied by 1.11 equals 109.89) and cash representing 0.89 of a share of Brooks common stock.
		In addition to shares of Brooks common stock and a cash payment for any fractional shares, Brooks will issue to holders of Helix common stock one preferred stock purchase right for each share of Brooks common stock issued in the merger. The preferred stock purchase rights are attached to the Brooks common stock and trade with the Brooks common stock until a triggering event occurs. The preferred stock purchase rights are described in more detail in the section entitled “DESCRIPTION OF BROOKS CAPITAL STOCK — Rights Agreement” beginning on page 101.
		If the merger is consummated, Helix common stock will no longer be traded publicly, and the combined company will continue to be traded on The Nasdaq National Market, under the symbol “BRKS.”
		If the merger is consummated, Brooks stockholders will continue to hold their existing Brooks common stock. Based upon the outstanding Brooks common stock and Helix common stock, and options to purchase Brooks common stock and Helix common stock, as of September 21, 2005, the current stockholders of Brooks are expected to own approximately 61% of the combined company and the current stockholders of Helix are expected to own approximately 39% of the combined company.
Q:		When and where will my company’s special meeting be held?
A:		Brooks. The Brooks special meeting will be held on October 26, 2005 at 9:00 a.m., local time, at Brooks’ offices at 15 Elizabeth Drive, Chelmsford, Massachusetts. See page 25.
		Helix. The Helix special meeting will be held on October 26, 2005 at 9:00 a.m., local time, at Palmer & Dodge LLP, 111 Huntington Avenue, Boston, Massachusetts. See page 28.
Q:		On what am I being asked to vote?
A:		Brooks. Brooks’ board of directors is asking Brooks stockholders to vote upon the following:
		1. A proposal, which is referred to in this joint proxy statement/ prospectus as the Brooks merger proposal, to approve the issuance of shares of Brooks common stock in the merger pursuant to the terms and conditions of the Agreement and Plan of Merger, dated as of July 11, 2005, among Brooks, Mt. Hood and Helix, as amended on August 29, 2005, which is referred to in this joint proxy statement/ prospectus as the merger agreement (see page 31);

iv

---

Table of Contents

		2. A proposal to approve an amendment to Brooks’ certificate of incorporation if the merger is consummated to increase Brooks’ authorized shares of common stock from 100,000,000 shares to 125,000,000 shares (see page 108); and
		3. A proposal to permit Brooks’ board of directors or its chairman, in its or his discretion, to adjourn or postpone the Brooks special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve either of the foregoing proposals (see page 110).
		Helix. Helix’s board of directors is asking Helix stockholders to vote upon the following:
		1. A proposal, which is referred to in this joint proxy statement/ prospectus as the Helix merger proposal, to adopt the merger agreement (see page 31); and
		2. A proposal to permit Helix’s board of directors or its chairman, in its or his discretion, to adjourn or postpone the Helix special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve the Helix merger proposal (see page 111).
Q:		Why was the merger agreement amended?
A:		On August 29, 2005, Brooks and Helix amended the merger agreement to clarify the applicability of expense reimbursement in all situations in which a termination fee is payable.
Q:		Is the Brooks merger proposal conditioned upon approval of the proposal to amend Brooks’ certificate of incorporation to increase Brooks’ authorized shares of common stock?
A:		No. The Brooks merger proposal is not conditioned on the proposal to amend Brooks’ certificate of incorporation to increase the authorized shares of Brooks common stock. Although Brooks currently has sufficient authorized but unissued shares of common stock to consummate the merger, Brooks is seeking to amend its certificate of incorporation to increase the number of authorized shares. In connection with the merger, Brooks anticipates that it will issue approximately 29,016,209 shares of common stock and reserve an additional 779,914 shares of Brooks common stock for issuance upon the exercise of Helix options assumed in the merger, in each case based on the outstanding shares of Helix common stock and outstanding options to purchase Helix common stock as of September 21, 2005. As a result, after consummation of the merger, Brooks would only have approximately 12,739,139 authorized shares of common stock that are not already issued or reserved for issuance pursuant to Brooks’ equity incentive plans, warrants and convertible securities as of September 21, 2005. Brooks’ board of directors believes that it is advisable and in the best interests of the stockholders to have available additional authorized but unissued shares in an amount adequate to provide for future needs, such as stock incentive programs or future transactions that involve the issuance of Brooks common stock. The proposal to amend Brooks’ certificate of incorporation, however, is conditioned on the consummation of the merger. Accordingly, if the Brooks merger proposal is not approved or the merger is not consummated for any other reason, Brooks will not amend its certificate of incorporation, even if approved by Brooks stockholders. See page 109.
Q:		Who is eligible to vote at the special meetings?
A:		Brooks. Brooks stockholders are eligible to vote at the Brooks special meeting if they were stockholders of record at the close of business on September 21, 2005, the record date for the Brooks special meeting. See page 25.
		Helix. Helix stockholders are eligible to vote at the Helix special meeting if they were stockholders of record at the close of business on September 21, 2005, the record date for the Helix special meeting. See page 28.
Q:		What votes are needed?
A:		Brooks. The affirmative vote of a majority of the votes properly cast on the proposal by holders of Brooks common stock is required to approve the Brooks merger proposal. The affirmative vote of a majority of the shares of Brooks common stock outstanding on the record date is required to approve

v

---

Table of Contents

		an amendment to the Brooks certificate of incorporation if the merger is consummated to increase Brooks’ authorized shares of common stock from 100,000,000 shares to 125,000,000 shares. The affirmative vote of a majority of the votes properly cast on the proposal by holders of Brooks common stock is required to permit Brooks’ board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary to solicit further proxies in favor of the foregoing proposals. At the Brooks special meeting, each share of Brooks common stock is entitled to one vote per share. See page 26.
		Helix. The affirmative vote of the holders of a majority of the shares of Helix common stock outstanding on the record date is required to approve the Helix merger proposal. The affirmative vote of the holders of a majority of the shares of Helix common stock present at the Helix special meeting in person or by proxy and entitled to vote on the proposal is required to permit Helix’s board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary to solicit further proxies in favor of the Helix merger proposal. Each share of Helix common stock has one vote per share. See page 28.
Q:		How do my company’s directors and executive officers intend to vote?
A:		Brooks. Brooks’ directors and executive officers have indicated that they intend to vote their shares of Brooks common stock “FOR” all the proposals to be voted on by Brooks stockholders. At the close of business on September 21, 2005, the record date for the Brooks special meeting, directors and executive officers of Brooks and their affiliates beneficially owned and were entitled to vote, or shared the right to vote, approximately 4.75% of the shares of Brooks common stock outstanding on that date. See page 26.
		Helix. Helix’s directors and executive officers have indicated that they intend to vote their shares of Helix common stock “FOR” all the proposals to be voted on by Helix stockholders. At the close of business on September 21, 2005, the record date for the Helix special meeting, directors and executive officers of Helix and their affiliates beneficially owned and were entitled to vote, or shared the right to vote, approximately 1.59% of the shares of Helix common stock outstanding on that date. See page 29.
Q:		Are there risks associated with the merger that I should consider in deciding how to vote?
A:		Yes. Among other things, the combined company may not achieve the expected benefits of the merger because of the risks and uncertainties discussed in the sections entitled “RISK FACTORS” beginning on page 18 and “CAUTIONARY STATEMENT CONCERNING FORWARD-LOOKING STATEMENTS” on page 24. Those risks include risks relating to the uncertainty that Brooks and Helix will be able to integrate their businesses successfully, uncertainties as to whether the combined company will achieve synergies expected to result from the merger, and uncertainties relating to the performance of the combined company following the merger.
Q:		Are any governmental approvals conditions to the closing of the merger?
A:		Yes. The merger is subject to review by the Antitrust Division of the U.S. Department of Justice, which is referred to in this joint proxy statement/ prospectus as the Antitrust Division, and the U.S. Federal Trade Commission, which is referred to in this joint proxy statement/ prospectus as the FTC, to determine whether it complies with the applicable antitrust laws. Under the provisions of the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended, which is referred to in this joint proxy statement/ prospectus as the HSR Act, the merger may not be consummated until the applicable waiting period requirements of the HSR Act have been satisfied. The waiting period expired on September 2, 2005. Each state and foreign country in which Brooks or Helix has operations also may review the merger under applicable state or foreign antitrust laws.
Q:		Do I have appraisal rights?
A:		No. Neither Brooks stockholders nor Helix stockholders have appraisal rights in the merger. See page 63.

vi

---

Table of Contents

Q:		Will my rights as a stockholder change as a result of the merger?
A:		Brooks. No. After the merger, Brooks stockholders will continue to hold shares of Brooks common stock, the rights of which are, and will continue to be, governed by Brooks’ certificate of incorporation and bylaws and the Delaware General Corporation Law, which is referred to in this joint proxy statement/ prospectus as the DGCL. See page 103.
		Helix. Yes. Although, like Helix, Brooks is a Delaware corporation, the Brooks certificate of incorporation and bylaws contain different provisions than the Helix certificate of incorporation and bylaws. See page 103 for a comparison of stockholder rights. To obtain a copy of Brooks’ current certificate of incorporation and bylaws, follow the directions provided in the section entitled “WHERE YOU CAN FIND MORE INFORMATION” on page 115.
Q:		When do you expect to complete the merger?
A:		If the merger proposals are approved at the special meetings, we expect to complete the merger as soon as possible after the satisfaction of the conditions to the merger. We currently anticipate that the merger will be completed in October 2005.
Q:		What should I do now?
A:		After carefully reading and considering the information contained in this joint proxy statement/ prospectus, please vote by one of the methods described below. The methods of voting that are available to you and instructions on how to vote your proxy in that manner will be explained in the instructions included with your proxy card or in materials you receive from your broker or other nominee.
		• Internet: by accessing the Internet website specified on your proxy card or supplied to you by your broker;
		• Telephone: by calling the toll-free number specified on your proxy card or supplied to you by your broker;
		• Mail: by completing, signing and dating your proxy card and returning it in the enclosed postage paid envelope; or
		• In Person: by attending your company’s special meeting.
Q:		If I am not going to attend my special meeting, should I return my proxy card(s)?
A:		Yes. Returning your signed and dated proxy card(s) ensures that your shares will be represented and voted at your special meeting, even if you are unable to or do not attend. Instead of returning your proxy card(s), you may vote by proxy by calling a toll-free telephone number or by using the Internet as described in the instructions included with the Brooks or Helix proxy card, as the case may be. See pages 26 and 29.
Q:		What if my shares are held in “street name” by my broker?
A:		Your broker will vote your shares at your special meeting only if you provide written instructions to your broker on how to vote. You should instruct your broker using the instruction form and envelope provided by your broker. If you do not provide your broker with instructions, your broker will not be authorized to vote with respect to the applicable proposals at your special meeting, other than the proposals regarding adjournments. A number of banks and brokerage firms participate in a program that also permits stockholders whose shares are held in “street name” to direct their vote by the Internet or telephone. This option, if available, will be reflected in the voting instructions from the bank or brokerage firm that accompany this joint proxy statement/ prospectus. If your shares are held in an account at a bank or brokerage firm that participates in such a program, you may direct the vote of these shares by the Internet or telephone by following the voting instructions enclosed with the proxy form from the bank or brokerage firm. If you hold your shares in your broker’s name and wish to vote in person at your special meeting, you must contact your broker and request a document called a “broker’s proxy.” You must bring this broker’s proxy to your special meeting in order to vote in person. See pages 26 and 29.

vii

---

Table of Contents

Q:		How will my proxy be voted?
A:		If you complete, sign and date your proxy card(s), or, if available, grant your proxy by telephone or the Internet, your shares will be voted in accordance with your instructions. If you sign and date your proxy card(s) but do not indicate how you want to vote, your shares will be voted “FOR” the proposals at your special meeting. See pages 26 and 29.
Q:		What if I abstain from voting, do not vote or do not instruct my broker to vote?
A:		Brooks. If a Brooks stockholder abstains, does not vote or does not instruct a broker how to vote shares of Brooks common stock held in street name, i.e., “broker non-votes,” it will have no effect on the vote to approve the Brooks merger proposal or to permit the adjournment or postponement of the Brooks special meeting if necessary to solicit further proxies in favor of the other proposals, and it will have the same effect as a vote against the amendment to the Brooks certificate of incorporation to increase the number of authorized shares of Brooks common stock. See page 26.
		Helix. If a Helix stockholder does not vote or does not instruct a broker how to vote shares of Helix common stock held in street name, i.e., “broker non-votes,” it will have the same effect as a vote against the Helix merger proposal, and it will have no effect on the proposal to permit the adjournment or postponement of the Helix special meeting if necessary to solicit further proxies in favor of the Helix merger proposal. If a Helix stockholder abstains from voting, it will have the same effect as a vote against the proposal with respect to which the stockholder abstained. See page 29.
Q:		Can I change my vote after I mail my proxy card(s) or, if available, vote by telephone or the Internet?
A:		Yes. You can change your vote at any time before your proxy is voted at the special meeting. To revoke your proxy, you must either (1) notify the corporate secretary of Brooks or Helix, as applicable, in writing, (2) submit a new proxy card dated after the date of the proxy you wish to revoke, (3) submit a later dated proxy over the Internet or by telephone by following the instructions on your proxy card or supplied to you by your broker or (4) attend the special meeting and vote your shares in person. Please note that if you vote over the Internet or by telephone, you may not be able to revoke or change your vote after a date prior to the date of the special meeting set forth in the instructions to voting in this manner. Merely attending the special meeting will not constitute revocation of your proxy. If your shares are held in street name by your broker, you will need to contact your broker to revoke your proxy. See pages 26 and 29.
Q:		Should stockholders send in their stock certificates now?
A:		No. Please do not send in your stock certificates with your proxy card. If the merger is completed, Helix stockholders will be sent written instructions for sending in their stock certificates. Brooks stockholders will not need to send in their stock certificates, even if the merger is completed. See page 68.
Q:		What does it mean if I receive multiple proxy cards?
A:		Your shares may be registered in more than one account, such as brokerage accounts and employee stock ownership plan accounts. It is important that you complete, sign, date and return each proxy card you receive, or, if available, vote by proxy using the telephone or the Internet as described in the instructions included with each proxy card you receive.

viii

---

Table of Contents

Q:		Who can answer my questions?
A:		If you have any questions about the merger or the special meetings, need assistance in voting your shares, or need additional copies of this joint proxy statement/ prospectus or the enclosed proxy card(s) or voting instructions, you should contact:

	If you are a Brooks stockholder:

	D. F. King & Co., Inc.
	48 Wall Street
	New York, NY 10005
	(800) 549-6746 (toll free)
	(212) 269-5550 (call collect)
	or
	Brooks Automation, Inc.
	15 Elizabeth Drive
	Chelmsford, Massachusetts 01824
	Attention: Director of Investor Relations
	Telephone: (978) 262-2400

	If you are a Helix stockholder:

	The Altman Group, Inc.
	1200 Wall Street West
	3rd Floor
	Lyndhurst, NJ 07071
	Holders: (866) 304-5477
	Bank/Brokers: (201) 806-7300

	Helix Technology Corporation
	Nine Hampshire Street
	Mansfield, Massachusetts 02048
	Attention: Investor Relations
	Telephone: (508) 337-5111

Q:		Where can I find more information about Brooks and Helix?
A:		You can find more information about Brooks and Helix from various sources described in the section entitled “WHERE YOU CAN FIND MORE INFORMATION” beginning on page 115.

ix

---

Table of Contents

1

---

Table of Contents

2

---

Table of Contents

3

---

Table of Contents

4

---

Table of Contents

5

---

Table of Contents

6

---

Table of Contents

7

---

Table of Contents

8

---

Table of Contents

9

---

Table of Contents

10

---

Table of Contents

11

---

Table of Contents

12

---

Table of Contents

13

---

Table of Contents

14

---

Table of Contents

15

---

Table of Contents

16

---

Table of Contents

17

---

Table of Contents

	The market value of the Brooks common stock that Helix stockholders will receive in the merger may be lower than expected.

	The merger is subject to conditions to closing that could result in the merger being delayed or not consummated, which could negatively impact Brooks’ or Helix’s stock price and future business and operations.

	Brooks and Helix may waive one or more of the conditions to the merger without resoliciting stockholder approval for the merger.

18

---

Table of Contents

	Directors and executive officers of Helix may have interests in the merger that are different from, or in addition to, the interests of Helix stockholders.

	Brooks and Helix will incur substantial expenses whether or not the merger is completed.

	Failure to complete the merger could negatively affect Brooks’ and Helix’s stock prices and each company’s future business and operations.

	Uncertainty regarding the merger and the effects of the merger could adversely affect each company’s relationships with its customers, suppliers, and strategic partners.

19

---

Table of Contents

	Brooks and Helix both depend on key personnel, and the loss of any of these key personnel because of uncertainty regarding the merger could hurt the businesses of Brooks, Helix or the combined company because of these employees’ experience in the automation, vacuum technology and/or semiconductor industries.

	The merger agreement limits Helix’s ability to pursue an alternative transaction proposal to the merger and requires Helix to pay a termination fee and reimburse Brooks for its transaction expenses if it does.

	The merger may result in additional limitations on Brooks’ ability to use its net operating loss carryforwards.

20

---

Table of Contents

	Brooks and Helix may be unable to successfully integrate their operations and realize the full cost savings each company anticipates.

	•	the challenge of effecting integration while carrying on an ongoing business;
	•	the necessity of coordinating geographically separate organizations;
	•	retaining and integrating personnel with diverse business backgrounds and cultures;
	•	retaining existing customers and strategic partners of each company; and
	•	implementing and maintaining consistent standards, controls, procedures, policies and information systems.

	Brooks expects to incur substantial expenses related to the integration of Helix.

	•	constraints arising under U.S. federal or state antitrust laws, such as limitations on sharing of information, that may prevent or hinder Brooks from fully developing integration plans prior to regulatory approval;
	•	employee redeployment, relocation or severance, as well as reorganization or closures of facilities;
	•	consolidating and rationalizing information technology and administrative infrastructures;
	•	coordinating sales and marketing efforts to effectively communicate the capabilities of the combined company;
	•	preserving supply, marketing or other important relationships of both Brooks and Helix and resolving potential conflicts that may arise; and

21

---

Table of Contents

	•	minimizing the diversion of management’s attention from ongoing business concerns and successfully returning managers to regular business responsibilities from their integration planning activities.

	The market price of Brooks common stock may decline as a result of the merger.

	•	the integration of Brooks and Helix is not completed in a timely and efficient manner;
	•	the combined company does not achieve the expected benefits of the merger as rapidly or to the extent anticipated by financial or industry analysts or by investors;
	•	the effect of the merger on the combined company’s financial results is not consistent with the expectations of financial or industry analysts or of investors; or
	•	significant stockholders of Brooks and Helix decide to dispose of their shares of Brooks common stock following completion of the merger.

	If the merger is consummated but the proposal to amend Brooks’ certificate of incorporation is not approved, the ability of Brooks to issue additional shares of Brooks common stock would be limited.

	Helix and Brooks stockholders will have a reduced ownership and voting interest after the merger and will exercise less influence over management.

22

---

Table of Contents

	Brooks may pursue additional acquisitions in the future.

	Brooks does not anticipate paying dividends.

	Following completion of the merger, the combined company will continue to face a number of risks related to its business that are currently faced by Brooks and Helix.

	•	the automation, vacuum and semiconductor industries, including cyclicality, technological change, and competition;
	•	the business and operations of each of Brooks and Helix, including research and development, manufacturing, and product development;
	•	concentration of customers and suppliers;
	•	protection of intellectual property;
	•	foreign business operations and international sales, including changes in a specific country’s or region’s political or economic conditions, laws and regulations that restrict repatriation of earnings, difficulty in recruiting trained personnel, language and cultural differences and changes in foreign currency exchange rates; and
	•	legal and regulatory matters.

23

---

Table of Contents

	•	the cyclical nature of the semiconductor industry and the markets addressed by each company’s products and its customers’ products;
	•	fluctuations in quarterly operating results;
	•	demand for and market acceptance of new and existing products and services;
	•	successful development of new products and services;
	•	the timing of new product and service introductions;
	•	reliance on a relatively small number of customers and suppliers;
	•	pricing pressures and other competitive factors;
	•	changes in product mix;
	•	product obsolescence;
	•	the ability to retain and hire key personnel;
	•	the ability to develop and implement new technologies and to obtain protection for the related intellectual property;
	•	the uncertainties of litigation, including intellectual property litigation in particular;
	•	costs related to the merger;
	•	failure to obtain the required approvals of Brooks stockholders and Helix stockholders;
	•	risks that the closing of the transaction will be substantially delayed or that the merger does not close; and
	•	the risk that Brooks’ and Helix’s businesses will not be integrated successfully or that expected benefits of the merger do not materialize.

24

---

Table of Contents

	•	To approve the issuance of shares of Brooks common stock pursuant to the Agreement and Plan of Merger, dated as of July 11, 2005, as amended on August 29, 2005, among Brooks, Mt. Hood and Helix, a copy of which is attached as Annex A to this joint proxy statement/ prospectus. This proposal is referred to in this joint proxy statement/ prospectus as the Brooks merger proposal;
	•	To approve a proposal to amend Brooks’ certificate of incorporation if the merger is consummated to increase Brooks’ authorized shares of common stock from 100,000,000 shares to 125,000,000 shares;
	•	To permit Brooks’ board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve either of the foregoing proposals; and
	•	To act upon such other matters as may properly come before the special meeting or any adjournments or postponements thereof.

25

---

Table of Contents

26

---

Table of Contents

27

---

Table of Contents

	•	To adopt the Agreement and Plan of Merger, dated as of July 11, 2005, as amended on August 29, 2005, among Brooks, Mt. Hood and Helix, a copy of which is attached as Annex A to this joint proxy statement/ prospectus. This proposal is referred to in this joint proxy statement/ prospectus as the Helix merger proposal;
	•	To permit Helix’s board of directors or its chairman, in its or his discretion, to adjourn or postpone the special meeting if necessary for further solicitation of proxies if there are not sufficient votes at the originally scheduled time of the special meeting to approve the Helix merger proposal; and
	•	To act upon such other matters as may properly come before the special meeting or any adjournments or postponements thereof.

28

---

Table of Contents

29

---

Table of Contents

30

---

Table of Contents

31

---

Table of Contents

32

---

Table of Contents

	•	A stock-for-stock transaction in which Helix stockholders would receive shares of the Second Company based on a 20% exchange ratio premium, subject to adjustment for any cash consideration agreed to by the parties. The outline did not include any specific ranges of possible cash consideration. Subsequent conversations indicated that the likely maximum cash consideration would not exceed $125.0 million in the aggregate, though the Second Company continued to consider whether it would include any cash. The outline provided that the transaction would be structured as a tax-free reorganization.
	•	A board of directors consisting of the existing seven Second Company directors, plus two directors to be nominated by Helix.
	•	The outline indicated that certain Helix employees would have a continued role in the combined entity; however, the outline did not contemplate the inclusion of any Helix officers in the senior management structure of the combined entity.

33

---

Table of Contents

34

---

Table of Contents

35

---

Table of Contents

36

---

Table of Contents

	•	consideration consisting of Brooks common stock based on a fixed exchange ratio that at the time of entering into a definitive agreement would imply a pro forma stock ownership in which Helix stockholders would own 39% of the combined company on a fully diluted basis;
	•	a management structure, as jointly recommended by the chief executive officers, consisting of Mr. Grady as the chief executive officer, Mr. Gentilcore as president of the hardware business and four other senior Helix operational executives having significant responsibilities in the combined entity; and
	•	a board of directors consisting of the existing seven Brooks directors, plus either three or four directors to be nominated by Helix.

37

---

Table of Contents

38

---

Table of Contents

39

---

Table of Contents

	•	the enhanced strategic and market position of the combined company beyond that achievable by Brooks alone;
	•	Brooks’ board of directors consideration of possible business combinations and other strategic alternatives;
	•	information concerning the business, operations, financial condition, earnings and prospects of Brooks as a separate entity and on a combined basis with Helix, including their revenues, their complementary businesses and the potential for revenue enhancement and cost savings;
	•	the increased volume, geographical expansion and diversity of operations, product lines, served markets and customers that could be achieved by combining Helix and Brooks;
	•	the opportunity for the combined company to combine complementary technologies to produce a more extensive set of offerings for their customers;
	•	the opportunity for Brooks stockholders to remain stockholders in a company that would be substantially larger as a result of the merger with a more diversified product line, a broader

40

---

Table of Contents

		customer base and enhanced technology capabilities, and to benefit from future growth of the combined company;
	•	the belief of Brooks’ board of directors that the subsystems, components and materials segment of the semiconductor industry is entering a consolidation phase and that the combined company, because of its scale and breadth of operations, would be in a better position to lead this consolidation;
	•	the ability of the combined company to evolve from a manufacturer and seller of components to a provider of subsystems and solutions, particularly in the automation and vacuum areas;
	•	the potential impact of the merger on Helix and Brooks customers;
	•	the likelihood of the merger being approved by the appropriate regulatory authorities;
	•	the corporate governance arrangements for Brooks following the merger, which initially will have a board of directors composed of eleven members, including three designated by Helix and one non-voting director emeritus designated by Helix, and the management structure of Brooks following the merger;
	•	the board of directors’ evaluation of the results of the due diligence investigations by Brooks’ management and legal and financial advisors;
	•	the structure of the merger and the terms of the merger agreement, which are reciprocal in nature, including the fact that the fixed exchange ratio provides relative certainty as to the number of shares of Brooks common stock to be issued in the merger;
	•	the fact that Brooks stockholders would hold approximately 61% of the outstanding common stock of the combined company after the merger;
	•	the then current financial market conditions and historical market prices, volatility and trading information with respect to Brooks common stock and Helix common stock;
	•	the combined company’s anticipated future financial performance, including the fact that the merger is expected to be accretive to Brooks’ earnings per share;
	•	the limited overlap of the product lines of Brooks and Helix;
	•	the opinion of Needham & Company, LLC, Brooks’ financial advisor, delivered to Brooks’ board of directors that, as of the date of the opinion and based on and subject to the assumptions and other matters described in the opinion, the exchange ratio pursuant to the merger agreement was fair, from a financial point of view, to Brooks; see the section entitled “Opinion of Brooks’ Financial Advisor” beginning on page 45. A copy of Needham & Company’s written opinion, dated July 10, 2005, is attached as Annex B to this joint proxy statement/prospectus and is incorporated by reference herein;
	•	the fact that the merger will be tax-free to Brooks stockholders for U.S. federal income tax purposes; and
	•	other potential strategic opportunities.

	•	the possibility that the expected benefits from the merger might not be fully realized;
	•	the possibility that the merger may not be consummated and the potential adverse consequences if the merger is not completed;
	•	the risk that the per share value of the consideration to be paid in the merger to Helix stockholders could increase significantly from the value prior to the announcement of the merger agreement

41

---

Table of Contents

		because the exchange ratio will not be adjusted for changes in the market price of Brooks common stock or Helix common stock;
	•	the challenges of integrating the management teams, strategies, cultures and organizations of the companies;
	•	the potential loss of customers and suppliers as a result of their unwillingness to do business with the combined company;
	•	the timing and receipt of government and regulatory approvals for the merger, and the possibility that delays in obtaining regulatory approvals of the merger could delay the closing;
	•	the fact that stockholder approval of the transaction would be required from both Helix and Brooks;
	•	the substantial expenses to be incurred in connection with the merger, including costs of integrating the businesses and transaction expenses arising from the merger; and
	•	the risk that key management and other personnel might not remain employed by the combined company.

	•	Helix’s board of directors’ consideration of possible business combinations and other strategic alternatives, as described further under the section captioned “— Background of the Merger,” including the process undertaken by Helix’s board of directors, with the assistance of Helix’s

42

---

Table of Contents

		management, financial advisor and legal counsel, to explore and review long-term strategic alternatives in the best interests of Helix stockholders;
	•	information concerning the business, operations, financial condition, earnings and prospects of each of Helix and Brooks as separate entities and on a combined basis, including their revenues, their complementary businesses and the potential for revenue enhancement and cost savings;
	•	the enhanced strategic and market position of the combined company and the combined company’s anticipated future financial performance;
	•	the limited overlap of the product lines of Helix and Brooks and the opportunity for the companies to combine complementary technologies to produce a more extensive set of offerings for their customers;
	•	the opportunity for Helix stockholders to participate in a combined company with increased scale, scope, technology capabilities and diversity of operations, product lines, served markets and customers beyond that achievable by Helix alone, and, as stockholders of the combined company, to benefit from future growth of the combined company;
	•	the belief of Helix’s board of directors that the subsystems, components and materials segment of the semiconductor industry is entering a consolidation phase and that the combined company, because of its scale and breadth of operations, would be in a better position to lead this consolidation;
	•	the ability of the combined company to evolve from a manufacturer and seller of components to a provider of subsystems and solutions, particularly in the automation and vacuum areas;
	•	the opportunity for Helix stockholders to continue to benefit from Helix’s tradition of operational excellence in the combined entity, through, in part, the retention of key executive officers of Helix in positions with significant operational responsibilities in the combined entity and the addition to Brooks’ board of directors of three new members and a director emeritus, each of whom is a current member of Helix’s board of directors;
	•	the then-current financial market conditions and historical market prices, volatility and trading information with respect to shares of Helix common stock and Brooks common stock;
	•	the exchange ratio negotiated with Brooks and the implied premium over recent and historical market prices of Helix common stock, as well as how this premium compared to price premiums in recent comparable transactions;
	•	the written opinion and related financial analyses of Morgan Stanley & Co. Incorporated, Helix’s financial advisor, that, as of the date of the opinion and based on and subject to the assumptions, factors and limitations set forth in the opinion, the exchange ratio pursuant to the merger agreement was fair from a financial point of view to holders of shares of Helix common stock. See the section entitled “— Opinion of Helix’s Financial Advisor” beginning on page 53. A copy of Morgan Stanley’s written opinion, dated July 10, 2005, is attached as Annex C to this joint proxy statement/ prospectus and is incorporated by reference herein;
	•	the structure of the merger and the terms and conditions of the merger agreement, which are reciprocal in nature, including the fact that the fixed exchange ratio provides certainty as to the number of shares of Brooks common stock to be issued in the merger;
	•	the provisions in the merger agreement that permit Helix’s board of directors to withdraw its recommendation that Helix stockholders approve the Helix merger proposal and to respond to unsolicited third-party proposals, and the belief of Helix’s board of directors, after consultation with its legal counsel and financial advisors, that these provisions, notwithstanding the obligation to pay a termination fee and reimburse expenses of the other party under certain circumstances, should not preclude the possibility of considering any competing transactions;

43

---

Table of Contents

	•	the likelihood of the merger being approved by the appropriate regulatory authorities;
	•	the fact that the merger will be tax-free to Helix stockholders for U.S. federal income tax purposes, except to the extent that Helix stockholders recognize gain on cash received for any fractional shares; and
	•	the results of due diligence investigations of Brooks by Helix’s management, independent auditors, financial advisors and legal counsel.

	•	the possibility that the merger may not be consummated and the potential adverse consequences if the merger is not completed;
	•	the risk that expected benefits from the merger will not be achieved;
	•	the risk that the per share value of the consideration to be paid to or received by Helix stockholders in the merger could decrease significantly from the value prior to the announcement of the merger agreement because the exchange ratio will not be adjusted for changes in the market price of Brooks common stock or Helix common stock;
	•	the possibility that Helix’s and Brooks’ businesses would be adversely affected, during the period from signing the merger agreement until integration is substantially implemented, by competitive pressures, the disruption inherent in combining two large businesses and the diversion of Helix’s management from other strategic initiatives;
	•	the potential loss of customers and suppliers and termination of contracts of either company as a result of a customer’s, supplier’s, or other counterparty’s unwillingness to do business with the combined company;
	•	the challenges and costs of integrating the assets, operations, management teams, strategies, cultures and organizations of the companies;
	•	the risk that key management and other personnel might not remain employed by the combined company;
	•	the timing and receipt of governmental and regulatory approvals for the merger, and the possibility that delays in obtaining regulatory approvals of the merger could delay the closing;
	•	if, once initiated, the merger is not ultimately consummated, this fact could have the effect of depressing values offered by others to Helix in a business combination and could erode customer and employee confidence in Helix;
	•	the fact that stockholder approval of the transaction would be required from both Helix and Brooks; and
	•	the interests of Helix’s executive officers and directors with respect to the merger may be different from, or in addition to, the interests of Helix common stockholders, as described in the section entitled “— Interests of Helix’s Directors and Executive Officers in the Merger” beginning on page 59.

44

---

Table of Contents

	•	reviewed the merger agreement;
	•	reviewed certain publicly available information concerning Brooks and Helix and certain other relevant financial and operating data of Brooks and Helix furnished to Needham & Company by Brooks and Helix;
	•	reviewed the historical stock prices and trading volumes of Brooks common stock and Helix common stock;
	•	held discussions with members of management of Brooks and Helix concerning their current and future business prospects and joint prospects for the combined company, including the potential cost savings and other synergies that may be achieved by the combined company;
	•	reviewed certain research analyst projections with respect to Brooks and held discussions with members of management of Brooks concerning those projections;
	•	reviewed certain research analyst projections with respect to Helix and held discussions with members of management of Helix concerning those projections;
	•	compared certain publicly available financial data of companies whose securities are traded in the public markets and that Needham & Company deemed relevant to similar data for Helix;

45

---

Table of Contents

	•	reviewed the financial terms of certain other business combinations that Needham & Company deemed generally relevant; and
	•	performed and considered such other studies, analyses, inquiries and investigations as Needham & Company deemed appropriate.

	Average Stock Price Ratio Analysis

46

---

Table of Contents

	•	The average stock price ratios for the prior 15 trading days, 30 trading days, 60 trading days, 90 trading days, 180 trading days, 12 months, two years, three years and five years. “Average stock price ratio” data represent the daily closing stock price of Helix common stock divided by the daily closing stock price of Brooks common stock averaged over the respective period.
	•	The implied deal premium to the average stock price ratio, which is equal to the percentage by which the exchange ratio pursuant to the merger agreement, 1.11 shares of Brooks common stock for each share of Helix common stock, exceeds the average stock price ratio for the specified periods.

		Average				Implied
Date or Period		Stock Price Ratio				Deal Premium
Last 15 trading days			0.875				26.8%
Last 30 trading days			0.866				28.1%
Last 60 trading days			0.896				23.9%
Last 90 trading days			0.940				18.1%
Last 180 trading days			0.953				16.5%
Last 12 months			0.973				14.1%
Last two years			0.960				15.6%
Last three years			0.939				18.2%
Last five years			0.836				32.8%
July 8, 2005							24.6%

	Contribution Analysis

47

---

Table of Contents

			Implied
			Actual/Estimated
			Percentage
			Contribution
			Brooks				Helix
Combined revenues
	FY2004A			77.5%				22.5%
	FY2005E			75.1%				24.9%
	FY2006E			74.0%				26.0%
Combined gross profit
	FY2004A			76.7%				23.3%
	FY2005E			72.3%				27.7%
	FY2006E			71.5%				28.5%
Combined EBITDA
	FY2004A			73.5%				26.5%
	FY2005E			64.5%				35.5%
	FY2006E			65.8%				34.2%
Combined EBIT
	FY2004A			72.0%				28.0%
	FY2005E			60.1%				39.9%
	FY2006E			65.1%				34.9%
Combined earnings before taxes
	FY2004A			65.2%				34.8%
	FY2005E			51.2%				48.8%
	FY2006E			61.3%				38.7%
Combined balance sheet data:
	Combined cash and equivalents			92.6%				7.4%
	Combined total assets			79.1%				20.9%
	Combined long term debt			100.0%				0.0%
	Combined stockholders’ equity			68.9%				31.1%
	Combined working capital net of debt			74.3%				25.7%
	Combined net cash			86.1%				13.9%

		Estimated Pro Forma
		Ownership in the
		Combined Company
		Brooks				Helix
		Stockholders				Stockholders
			61.0%				39.0%

	Pro Forma Transaction Analysis

48

---

Table of Contents

	Selected Company Analysis

	Advanced Energy Industries, Inc.
	Asyst Technologies, Inc.
	ATMI, Inc.
	Cymer, Inc.
	Entegris, Inc.
	INFICON Holding AG
	MKS Instruments, Inc.
	Mykrolis Corporation
	Ultra Clean Holdings, Inc.

	•	Enterprise value as a multiple of last 12 months, which is referred to in this joint proxy statement/ prospectus as LTM, revenues;
	•	Enterprise value as a multiple of projected calendar year 2005 revenues;
	•	Enterprise value as a multiple of projected calendar year 2006 revenues;
	•	Enterprise value as a multiple of LTM EBITDA;
	•	Enterprise value as a multiple of LTM EBIT;
	•	Price as a multiple of LTM EPS;
	•	Price as a multiple of projected calendar year 2005 EPS;
	•	Price as a multiple of projected calendar year 2006 EPS;
	•	Enterprise value as a multiple of net assets; and
	•	Market value as a multiple of book value.

49

---

Table of Contents

Selected Companies

Implied

Helix at

High

Low

Mean

Median

Offer

Enterprise value to LTM revenues

3.9x

0.5x

1.5x

1.3x

2.7x

Enterprise value to projected calendar year 2005 revenues

3.5x

0.6x

1.5x

1.4x

2.4x

Enterprise value to projected calendar year 2006 revenues

3.1x

0.5x

1.4x

1.1x

2.1x

Enterprise value to LTM EBITDA

23.1x

7.3x

12.7x

11.3x

21.1x

Enterprise value to LTM EBIT

24.8x

8.5x

15.5x

14.5x

29.2x

Price as a multiple of LTM EPS

37.9x

14.3x

24.0x

23.4x

18.4x

Price as a multiple of projected calendar year 2005 EPS

40.6x

13.3x

28.4x

28.8x

35.3x

Price as a multiple of projected calendar year 2006 EPS

68.4x

11.7x

24.1x

19.1x

25.2x

Enterprise value to net assets

2.4x

1.0x

1.5x

1.3x

3.0x

Market value to book value

3.6x

1.3x

2.2x

2.0x

3.2x

	Stock Price Premium Analysis

		Selected Transactions
																		Brooks/Helix
		High				Low				Mean				Median				Merger
One day stock price premium			71.0%				1.1%				27.2%				23.6%				24.6%
One week stock price premium			68.1%				3.4%				29.5%				25.0%				32.7%
One month stock price premium			72.0%				1.9%				37.8%				38.3%				27.5%

50

---

Table of Contents

	Selected Transaction Analysis

Target		Acquirer
Align-Rite International, Inc.		Photronics, Inc.
Applied Science and Technology, Inc.		MKS Instruments, Inc.
Cerprobe Corporation		Kulicke and Soffa Industries, Inc.
CFM Technologies, Inc.		Mattson Technology, Inc.
CoorsTek, Inc.		Keystone Holdings LLC (Coors Family)
CVC, Inc.		Veeco Instruments Inc.
DuPont Photomasks, Inc.		Toppan Printing Co., Ltd.
GaSonics International Corporation		Novellus Systems, Inc.
GenRad, Inc.		Teradyne, Inc.
Genus, Inc.		Aixtron AG
Integrated Measurement Systems, Inc.		Credence Systems Corporation
NPTest Holding Corporation		Credence Systems Corporation
Numerical Technologies, Inc.		Synopsys, Inc.
Plasma-Therm, Inc.		Oerlikon-Bührle Holding AG
PRI Automation, Inc.		Brooks Automation, Inc.
SpeedFam-IPEC, Inc.		Novellus Systems, Inc.

	•	aggregate transaction value as a multiple of LTM revenues;
	•	aggregate transaction value as a multiple of LTM EBIT;
	•	aggregate transaction value as a multiple of LTM EBITDA;
	•	transaction value as a multiple of LTM net income; and
	•	transaction value as a multiple of book value.

Selected Transactions

Brooks/Helix

High

Low

Mean

Median

Merger

Aggregate transaction value to LTM revenues

4.0x

0.8x

2.4x

2.2x

2.7x

Aggregate transaction value to LTM EBIT

21.9x

11.3x

16.4x

16.3x

29.2x

Aggregate transaction value to LTM EBITDA

44.6x

8.3x

17.0x

11.8x

21.1x

Transaction value to LTM net income

32.1x

16.2x

23.7x

23.2x

18.4x

Transaction value to book value

11.0x

1.2x

3.5x

2.5x

3.2x

51

---

Table of Contents

52

---

Table of Contents

	•	reviewed certain publicly available financial statements and other business and financial information of Helix and Brooks;
	•	reviewed certain internal financial statements and other financial and operating data concerning Helix and Brooks prepared by the managements of Helix and Brooks, respectively;
	•	reviewed certain financial projections prepared by the managements of Helix and Brooks;
	•	discussed the past and current operations, financial condition and prospects of Helix and Brooks with senior executives of Helix and Brooks, respectively;
	•	reviewed the pro forma impact of the merger on Brooks’ earnings per share;
	•	discussed potential strategic, financial and operational benefits anticipated from the merger with senior executives of Helix and Brooks;
	•	reviewed reported prices and trading activity for Helix common stock and Brooks common stock;
	•	compared the financial performance of Helix and Brooks and prices and trading activity of Helix common stock and Brooks common stock with those of certain other comparable publicly traded companies;
	•	reviewed the financial terms, to the extent publicly available, of certain comparable acquisition transactions;
	•	participated in discussions and negotiations among representatives of Helix and Brooks and their financial and legal advisors;
	•	reviewed the merger agreement and certain related documents; and
	•	performed such other analyses and considered such other factors as Morgan Stanley deemed appropriate.

53

---

Table of Contents

	Historical Common Stock Performance

	Comparative Stock Price Performance

54

---

Table of Contents

	Exchange Ratio Premium Analysis

						July 8, 2005 Market Exchange
						Ratio (0.891x) Premium/				Merger Exchange Ratio (1.11x)
		Period Average				(Discount) to Period Average				Premium/ (Discount) to Period
Period		Exchange Ratio				Exchange Ratio				Average Exchange Ratio
July 8, 2005			0.891	x			0.0	%			24.6	%
Last 30 Trading Days			0.866				2.9				28.1
Last 60 Trading Days			0.896				(0.5	)			23.9
Last 90 Trading Days			0.940				(5.2	)			18.1
Since July 8, 2004			0.973				(8.5	)			14.0
High Since July 8, 2004			1.171				(23.9	)			(5.2	)
Low Since July 8, 2004			0.818				8.9				35.6

	Relative Contribution Analysis

		Percentage
		Contribution
		Brooks				Helix
Estimated Net Income
Fiscal Year Ending September 30, 2006			59.9	%			40.1	%
Twelve Months Ending June 30, 2006			63.1				36.9
Estimated Operating Income
Fiscal Year Ending September 30, 2006			59.6	%			40.4	%
Twelve Months Ending June 30, 2006			62.4				37.6
Estimated Revenue
Fiscal Year Ending September 30, 2006			71.9	%			28.1	%
Twelve Months Ending June 30, 2006			72.9				27.1

			Percentage Implied Ownership
			of the Combined Company
			Brooks Stockholders				Helix Stockholders
Estimated Net Income
	Fiscal Year Ending September 30, 2006			59.9	%			40.1	%
	Twelve Months Ending June 30, 2006			63.1				36.9
Estimated Operating Income
	Fiscal Year Ending September 30, 2006			64.6	%			35.4	%
	Twelve Months Ending June 30, 2006			66.9				33.1
Estimated Revenue
	Fiscal Year Ending September 30, 2006			74.6	%			25.4	%
	Twelve Months Ending June 30, 2006			75.4				24.6

55

---

Table of Contents

	Present Value of Research Analyst Price Targets Analysis

	Comparable Company Analysis

										Aggregate Value/
		Price/ Earnings								Revenue
Company		CY2005E				CY2006E				CY2005E				CY2006E
Advanced Energy Industries, Inc.			32.3				10.8				0.9				0.8
Entegris, Inc.			34.1				31.7				1.9				1.8
MKS Instruments, Inc.			29.5				18.6				1.4				1.3
Pfeiffer Vacuum Technology AG			16.0				14.9				1.7				1.6

56

---

Table of Contents

	Precedent Transactions Analysis

		Premium to:
						30-Day Average				30-Day Average
		One Day				Stock Price				Historical Exchange Ratio
		Before Announcement				Before Announcement				Before Announcement
Mean			21	%			22	%			12	%
Median			21				22				13

		Premium to:
						30-Day Average				30-Day Average
		One Day				Stock Price				Historical Exchange Ratio
		Before Announcement				Before Announcement				Before Announcement
Mean			30	%			24	%			22	%
Median			29				22				24

57

---

Table of Contents

	Pro Forma Analysis of the Merger

		Estimated Pro Forma Fiscal 2006
Fiscal 2006 Pretax Synergies		Brooks Earnings per Share				Accretion
No Synergies		$	0.71			$	0.05
$5.0 Million Pretax Synergies			0.76				0.11
$7.5 Million Pretax Synergies			0.79				0.13
$10.0 Million Pretax Synergies			0.82				0.16

58

---

Table of Contents

	Governance Structure

	Stock Options

	Existing Employment Arrangements with Helix

59

---

Table of Contents

	Employment Arrangements with Brooks

60

---

Table of Contents

	Indemnification and Insurance

61

---

Table of Contents

62

---

Table of Contents

63

---

Table of Contents

	•	a United States citizen or resident alien as determined under the Internal Revenue Code;
	•	a corporation, as defined by the Internal Revenue Code, that is organized under the laws of the United States, any state or the District of Columbia;
	•	an estate, the income of which is subject to United States federal income taxation regardless of its source; or
	•	a trust, if (1) a court within the United States is able to exercise primary supervision over its administration and at least one United States person is authorized to control all of its substantial decisions or (2) it has a valid election in effect, under applicable United States treasury regulations, to be treated as a United States person.

64

---

Table of Contents

	Exchange of Helix Common Stock

	•	A holder of Helix common stock will not recognize any gain or loss upon the receipt of Brooks common stock in exchange for Helix common stock in the merger, except to the extent of cash received in lieu of a fractional share.
	•	A Helix stockholder’s aggregate tax basis in Brooks common stock received in the merger in exchange for Helix common stock will be the same as the aggregate basis of the Helix common stock surrendered in the exchange, reduced by the portion of the adjusted basis in Helix common stock that is allocable to any fractional share of Brooks common stock for which cash is received.
	•	A Helix stockholder’s holding period for the Brooks common stock received in the merger in exchange for such stockholder’s Helix common stock will include the holding period for the Helix common stock surrendered in the exchange.
	•	A Helix stockholder that receives cash in lieu of a fractional share of Brooks common stock will generally recognize capital gain or loss equal to the difference between the cash received in lieu of such fractional share and the portion of the stockholder’s adjusted tax basis in Helix common stock surrendered that is allocable to such fractional share. The capital gain or loss will be long-term capital gain or loss if the holding period for Helix common stock exchanged for cash in lieu of the fractional share of Brooks common stock is more than one year at the time of the merger.
	•	None of Brooks, Helix, or any stockholder of Brooks will recognize any gain or loss as a result of the transaction.

65

---

Table of Contents

66

---

Table of Contents

67

---

Table of Contents

	•	pay any transfer or other taxes required because the payment is made to a person other than the registered holder of the Helix stock certificate; or
	•	establish to the satisfaction of the exchange agent that any transfer or other taxes described above have been paid or are not applicable.

68

---

Table of Contents

	1. the party and its subsidiaries’ assets, business, results of operations, properties or financial condition, taken as a whole; or
	2. the party’s or its subsidiaries’ ability to complete the transactions contemplated by the merger agreement on the terms set forth in the merger agreement.

	•	conditions affecting the regional, national or global economy or securities markets in general that do not have a materially disproportionate impact on the party and its subsidiaries;
	•	conditions affecting the industry in which the party and its subsidiaries operate generally that do not have a materially disproportionate impact on the party and its subsidiaries;
	•	any change in the stock price or trading volume of the party’s common stock, except that the facts or occurrences giving rise to or contributing to such change may be taken into account;
	•	any act of terrorism or war not specifically directed at the party that does not have a materially disproportionate impact on the party;
	•	the announcement of the merger agreement and the transactions contemplated by the merger agreement;
	•	actions taken or omissions to act with the prior written consent of the other party;
	•	changes in laws of general applicability or interpretations by courts or other governmental entities that do not have a materially disproportionate impact on the party and its subsidiaries; or
	•	changes in generally accepted accounting principles.

	•	corporate organization and standing, the corporate power to carry on the representing party’s business and qualification to do business of the party and its respective subsidiaries;
	•	ownership of subsidiaries and joint ventures;
	•	capitalization;
	•	corporate power and authority to enter into the merger agreement and due execution, delivery and enforceability of the merger agreement;
	•	board of director approval of the merger agreement and the transactions contemplated by the merger agreement and the approvals required by the representing party’s stockholders;
	•	absence of conflicts with charter documents, absence of breaches of material contracts and agreements, absence of material liens upon assets and absence of violations of applicable law, in each case resulting from the execution, delivery and performance of the merger agreement and consummation of the transactions contemplated by the merger agreement;

69

---

Table of Contents

	•	absence of required governmental consents in connection with execution, delivery and performance of the merger agreement and consummation of the transactions contemplated by the merger agreement other than certain governmental filings specified in the merger agreement;
	•	timely filing of required documents with the SEC, material compliance with the requirements of the Securities Act and Exchange Act and the absence of untrue statements or material omissions in those documents;
	•	conformity of financial statements to generally accepted accounting principles and the adequacy of internal controls over financial reporting and disclosure controls and procedures;
	•	absence of certain undisclosed liabilities or obligations;
	•	absence of untrue or misleading information provided by the representing party contained or incorporated into this joint proxy statement/ prospectus or the registration statement of which this joint proxy statement/ prospectus forms a part;
	•	absence of specified changes or events after a specified date, and the conduct of the party’s and its subsidiaries’ respective businesses after such specified date;
	•	tax matters;
	•	material contracts;
	•	intellectual property matters;
	•	absence of litigation, court orders and investigations;
	•	possession of permits and licenses and compliance with applicable laws and permits and licenses;
	•	brokers’ or finders’ fees;
	•	employee benefits matters and compliance with the Employee Retirement Income Security Act of 1974;
	•	labor agreements and employee matters;
	•	environmental matters and compliance with environmental laws;
	•	insurance matters;
	•	relationships with customers, suppliers, collaborators, distributors, licensees and licensors;
	•	opinions of financial advisers;
	•	ownership of the other party’s stock by the representing party or its affiliates or associates;
	•	transactions with affiliates; and
	•	title to tangible assets and absence of certain liens on tangible assets, ownership of real property and leasehold interests in leased real property.

	Operating Covenants

70

---

Table of Contents

	•	dispose of significant amounts of assets;
	•	incur significant liabilities;
	•	increase or agree to increase the compensation payable to any director or employee, or enter into any employment agreement with any director or employee, except as required by law or existing employment agreement or in the case of compensation for employees other than officers or directors in the ordinary course of business consistent with past practice;
	•	make any change in the number of shares of its capital stock outstanding or grant or accelerate the exercisability of any convertible security, declare or pay any dividend, except that Helix may pay dividends in the ordinary course of business consistent with past practice, including with respect to timing and amount;
	•	issue or redeem any capital stock or securities exchangeable for or convertible into capital stock, other than upon the exercise of convertible securities outstanding on July 6, 2005 or in connection with grants of options to purchase common stock, limited to options to purchase 75,000 shares in the case of Helix;
	•	cause, permit or propose any amendment to its certificate of incorporation, except that Brooks may seek the authorization of additional shares of common stock, or elect or appoint any new directors or officers;
	•	make any significant acquisition, lease, investment or capital contribution other than in the ordinary course of business consistent with past practice;
	•	authorize significant capital expenditures;
	•	except for cash management activities, purchase any securities or make any investment;
	•	except as required as a result of a change in law or generally accepted accounting principles, change any of its accounting principles;
	•	take or permit any subsidiary to take any action that would prevent the merger from qualifying as a reorganization under the Internal Revenue Code;
	•	change any material tax election or settle or compromise any material tax liability, change any annual tax accounting period, enter into any closing agreement relating to any material tax refund or surrender any right to claim a material tax refund;
	•	commence, settle or compromise any pending or threatened suit, action or claim which is material to the party, relates to the merger and related transactions, would involve material restrictions on the party’s business or would involve the issuance of the party’s securities;
	•	adopt a plan of complete or partial liquidation, dissolution, merger, consolidation, restructuring or similar reorganization;
	•	satisfy any material claims, liabilities or obligations other than the payment of liabilities in the ordinary course of business;
	•	effectuate a “plant closing” or “mass layoff” as those terms are defined in the Worker Adjustment and Retraining Notification Act of 1988;
	•	enter into, terminate or materially modify any agreement required to be filed by such entity on its periodic reports filed with the SEC, other than those pertaining to compensation of management;
	•	fail to pay any fee, take any action or make any filing reasonably necessary to maintain material intellectual property rights;

71

---

Table of Contents

	•	in the case of Helix only, modify, amend, terminate or provide a release under any confidentiality or standstill agreement to which Helix is a party and which relates to a business combination involving Helix;
	•	amend, modify or waive any takeover defenses or take any action to render state takeover defenses inapplicable to any transaction other than the merger and related transactions; or
	•	obligate itself to do any of the foregoing.

	Additional Covenants

	•	filing a joint proxy statement and registration statement;
	•	providing the other company access to information and cooperating regarding filings with governmental and other agencies and organizations;
	•	making and maintaining the required recommendation by the respective boards of directors to their stockholders, subject to the rights of the boards of directors of each of Brooks and Helix to change that recommendation as discussed below;
	•	convening and holding special meetings of stockholders to vote on the merger proposals;
	•	obtaining governmental consents required to be obtained in connection with the merger;
	•	avoiding actions that would cause the transaction to fail to qualify as a tax-free reorganization under Section 368(a) of the Internal Revenue Code;
	•	using reasonable commercial efforts to obtain all necessary third-party consents in connection with the merger;
	•	using reasonable best efforts to take all actions that are necessary or advisable to consummate the transactions contemplated by the merger agreement;
	•	the listing of the Brooks common stock to be issued in the merger on The Nasdaq National Market and the delisting of the Helix common stock;
	•	confidentiality;
	•	matters relating to Section 16 of the Exchange Act;
	•	public announcements of the merger and the transactions contemplated by the merger agreement;
	•	notices of certain events; and
	•	refraining from acquiring the other party’s common stock.

	Affiliate Agreements

	Stock Plans and Other Options

72

---

Table of Contents

	Employee Benefit and Employee Matters

73

---

Table of Contents

	Conditions to Each Party’s Obligation to Effect the Merger

	•	approval of the Helix merger proposal by Helix stockholders and approval of the Brooks merger proposal by Brooks stockholders;
	•	the Form S-4 registration statement of which this joint proxy statement/ prospectus is a part must not be the subject of any stop order or proceedings seeking a stop order;
	•	no temporary restraining order, preliminary or permanent injunction, or other order issued by any court of competent jurisdiction or other legal or regulatory restraint or prohibition preventing the consummation of the merger has been issued;
	•	all consents, approvals and actions of, filings with and notices to any governmental entity required by Brooks, Helix or any subsidiary to consummate the merger, the failure of which to be obtained or taken is reasonably likely to have a material adverse effect, must have been obtained, filed or made, as applicable;
	•	no suit, action or proceeding by any governmental entity may be pending or threatened in writing challenging the merger agreement or the transactions contemplated by the merger agreement seeking to delay, restrain or prohibit the merger or seeking to obtain material damages from Brooks or Helix, seeking to prohibit or impose material limitations on the ownership or operation of all or a portion of the assets of Helix or Brooks or compel Brooks or Helix to dispose of or hold separately any material portion of its business;
	•	the waiting period, and any extensions thereof, applicable to the consummation of the merger under the HSR Act must have expired or been terminated and all applicable foreign antitrust and competition approvals in jurisdictions in which either Helix or Brooks have significant operations must have been received; and
	•	the shares of Brooks common stock must continue to be quoted on The Nasdaq National Market and the shares of Brooks common stock to be issued in the merger must have been approved for quotation on The Nasdaq National Market, subject to official notice of issuance.

	Additional Conditions to Obligations of Brooks

	•	the representations and warranties of Helix in the merger agreement must be true and correct as of the date of the merger agreement and immediately before the effective time of the merger, except representations or warranties that by their terms speak only as of an earlier date, which must be true and correct as of such earlier date, and except to the extent any inaccuracy in any such representation or warranty would not reasonably be likely to have, individually or in the aggregate, a

74

---

Table of Contents

		material adverse effect on Helix, provided that solely for purposes of this condition, any representation or warranty of Helix that is qualified by materiality or material adverse effect language must be read as if such language were not present; and Brooks must have received a certificate signed on behalf of Helix by the chief executive officer and chief financial officer of Helix to that effect;
	•	Helix must have performed in all material respects all obligations required to be performed by it under the merger agreement at or before the effective time of the merger, and Brooks must have received a certificate signed on behalf of Helix by the chief executive officer and the chief financial officer of Helix to that effect;
	•	Brooks must have received various certificates with respect to the existence and good standing of Helix and the authorization of the transaction by Helix’s board of directors and stockholders; and
	•	Brooks must have received from its counsel a tax opinion to the effect that on the basis of facts, representations and assumptions set forth or referred to in the opinion, the merger will be treated for federal income tax purposes as a reorganization within the meaning of Section 368(a) of the Internal Revenue Code.

	Additional Conditions to Obligations of Helix

	•	the representations and warranties of Brooks in the merger agreement must be true and correct as of the date of the merger agreement and immediately before the effective time of the merger, except representations or warranties that by their terms speak only as of an earlier date, which must be true and correct as of such earlier date, and except to the extent any inaccuracy in any such representation or warranty would not reasonably be likely to have, individually or in the aggregate, a material adverse effect on Brooks, provided that solely for purposes of this condition, any representation or warranty of Brooks that is qualified by materiality or material adverse effect language must be read as if such language were not present; and Helix must have received a certificate signed on behalf of Brooks by the chief executive officer and chief financial officer of Brooks to that effect;
	•	Brooks must have performed in all material respects all obligations required to be performed by it under the merger agreement at or before the effective time of the merger, and Helix must have received a certificate signed on behalf of Brooks by the chief executive officer and the chief financial officer of Brooks to that effect;
	•	Helix must have received various certificates with respect to the existence and good standing of Brooks and the authorization of the transaction by Brooks’ board of directors and stockholders; and
	•	Helix must have received from its counsel a tax opinion, to the effect that, on the basis of facts, representations and assumptions set forth or referred to in the opinion, the merger will be treated for federal income tax purposes as a reorganization within the meaning of Section 368(a) of the Internal Revenue Code.

	•	initiate, solicit or knowingly encourage any inquiries or proposals that constitute, or would be reasonably likely to lead to, a proposal or offer for an “acquisition proposal” as defined below;

75

---

Table of Contents

	•	enter into any agreement with respect to any acquisition proposal; or
	•	engage in negotiations or discussions with, or provide any information or data to any person or group other than Brooks or its affiliates concerning any acquisition proposal or grant any waiver or release under any standstill or other agreement.

	•	any acquisition or purchase from Helix of more than a 20% interest in Helix’s outstanding voting securities or any tender offer or exchange offer that if consummated would result in the acquisition of more than 20% of Helix’s outstanding voting securities, whether by purchase of stock, consolidation, business combination, merger or other similar transaction;
	•	any sale, lease, exchange, transfer, license, acquisition or disposition of assets of Helix, including the stock or assets of any subsidiary of Helix, for consideration equal to 20% or more than the aggregate fair market value of all outstanding shares of Helix common stock prior to the date of the merger agreement, whether by purchase of stock, consolidation, business combination, merger or other similar transaction; or
	•	any recapitalization, restructuring, liquidation or dissolution of Helix.

76

---

Table of Contents

	•	by the mutual written consent of Brooks and Helix;
	•	by either Brooks or Helix:

	•	if the merger has not been consummated on or before February 15, 2006, referred to in this joint proxy statement/ prospectus as the “termination date,” provided that the right to terminate the merger agreement because the termination date has passed is not available to any party whose action or failure to fulfill an obligation in the merger agreement has been the principal cause of the failure to consummate the merger prior to the termination date;
	•	if a court or other governmental entity has issued a final order or ruling not subject to appeal, or a statute or regulation has been enacted, that restrains or prohibits the merger or any of the other transactions contemplated by the merger agreement, provided that the party seeking to terminate the agreement on this basis must have used all reasonable efforts to prevent the entry of and to remove such order, ruling, statute or regulation; or
	•	if Brooks or Helix stockholders fail to give the necessary approvals described in this joint proxy statement/ prospectus at the special meeting called for that purpose or any adjournment of that meeting;

	•	by Brooks:

	•	if Helix has breached, or there is an inaccuracy in, any representation, warranty, covenant or agreement of Helix in the merger agreement which has resulted or is reasonably likely to result in any condition precedent to Brooks’ obligation to consummate the merger not being satisfied,

77

---

Table of Contents

		and if capable of cure, this breach or inaccuracy is not cured within 30 days after receipt of written notice from Brooks;
	•	if the board of directors of Helix has:

	•	withdrawn, modified or changed its approval of the merger agreement, publicly announced its intention to do so or failed to recommend that Helix stockholders approve the Helix merger proposal,
	•	approved or recommended to Helix’s stockholders, or publicly announced its intention to enter into any agreement with respect to, any acquisition proposal other than the merger with Brooks,
	•	resolved or publicly proposed to do any of the above, or
	•	failed to recommend against, or taken a neutral position with respect to, a tender or exchange offer related to an acquisition proposal in any position taken pursuant to Rule 14d-9 and 14e-2 under the Exchange Act; or

	•	if Helix has violated or breached in any material respect its non-solicitation obligations; and

	•	by Helix:

	•	if Brooks has breached, or there is an inaccuracy in, any representation, warranty, covenant or agreement of Brooks in the merger agreement which has resulted or is reasonably likely to result in any condition precedent to Helix’s obligation to consummate the merger not being satisfied, and if capable of cure, this breach or inaccuracy is not cured within 30 days after receipt of written notice from Helix;
	•	if the board of directors of Brooks has, or has publicly announced its intention to, withdrawn, modified or changed its approval or recommendation that Brooks stockholders approve the Brooks merger proposal, failed to recommend that Brooks stockholders approve the Brooks merger proposal or resolved or publicly proposed to do any of these things;
	•	if prior to the adoption and approval of the merger agreement by Helix stockholders:

	•	Helix has received a superior proposal,
	•	in light of this superior proposal, Helix’s board of directors has determined in good faith after consultation with outside counsel that it is necessary for it to withdraw, amend or modify its approval or recommendation that Helix stockholders approve the Helix merger proposal order to comply with its fiduciary duties,
	•	Helix has provided written notice of this determination to Brooks and attached a copy of the agreement containing all of the terms of the superior proposal to the notice,
	•	at least three business days have passed following receipt by Brooks of the notice described above, and after taking into account any revised proposal made by Brooks, Helix’s board of directors again determines in good faith after consultation with outside counsel that it is necessary for it to withdraw, amend or modify its approval or recommendation that Helix stockholders approve the Helix merger proposal in order to comply with its fiduciary duties,
	•	Helix has not breached its non-solicitation covenants in any material respect,
	•	concurrent with termination of the merger agreement pursuant to this provision, Helix enters into a definitive agreement providing for the implementation of a superior proposal, and
	•	at or prior to termination, Helix pays the termination fee described below.

78

---

Table of Contents

	•	the merger agreement is terminated because the termination date has passed and the Helix special meeting has not occurred, because of an intentional breach of the merger agreement by Helix or because of a failure by Helix stockholders to adopt the merger agreement;
	•	prior to the time of termination and after the date of the merger agreement, an acquisition proposal has been publicly announced or communicated to Helix’s board of directors; and,
	•	within 12 months after the date of termination, Helix enters into a definitive agreement with respect to an acquisition proposal or an acquisition proposal is consummated.

79

---

Table of Contents

80

---

Table of Contents

Name		Age				Position
Edward C. Grady			58			Chief Executive Officer and Director
James F. Gentilcore			53			President and Chief Operating Officer, Semiconductor Products Group
Joseph M. Bellini			45			President and Chief Operating Officer, Enterprise Software Group
Robert E. Anastasi			59			Executive Vice President, Global Operations
Thomas S. Grilk			58			Senior Vice President and General Counsel
Robert W. Woodbury, Jr.			48			Senior Vice President and Chief Financial Officer
Richard C. Small			47			Vice President and Corporate Controller
A. Clinton Allen			61			Director
Roger D. Emerick			65			Director
Amin J. Khoury			66			Director
Robert J. Lepofsky			60			Director
Joseph R. Martin			57			Director
John K. McGillicuddy			62			Director
Robert J. Therrien			70			Director
Alfred Woollacott, III			58			Director
Mark S. Wrighton			56			Director
Marvin G. Schorr			80			Director Emeritus

81

---

Table of Contents

82

---

Table of Contents

83

---

Table of Contents

	•	each person, including any partnership, syndicate, or other group, known to Brooks management to be the beneficial owner of more than five percent of the outstanding shares of Brooks common stock;
	•	each of Brooks’ directors;
	•	the individuals who qualify as Brooks’ “named executive officers” under the regulations of the SEC; and
	•	all of Brooks’ executive officers and directors as a group.

			Shares Beneficially
			Owned
							Percent of
Beneficial Owner			Number				Class
5% Stockholders
Mazama Capital Management(1)				6,376,370				14.32	%
	One Southwest Columbia, Suite 1500
	Portland, Oregon 97258
TCW Group, Inc.(2)				2,761,879				6.1	%
	865 South Figueroa St.
	Los Angeles, CA 90017
David Nierenberg(3)				2,571,156				5.7	%
	19605 NE 8th Street
	Camas, WA 98607
Barclays Global Investors NA(4)				2,235,355				5.0	%
	45 Fremont St., 17th FL
	San Francisco, CA 94105
Executive Officers and Directors
Robert J. Therrien(5)				1,352,436				2.94	%
Edward C. Grady(5)				339,296				*
Joseph Bellini(5)				97,555				*
Jeffrey A. Cassis(5)(6)				214,335				*
Peter Frasso(5)(6)				—				*
Robert W. Woodbury, Jr.(5)				121,713				*
Roger D. Emerick(5)				85,750				*
Amin J. Khoury(5)				61,750				*
Joseph R. Martin(5)				34,750				*

84

---

Table of Contents

		Shares Beneficially
		Owned
						Percent of
Beneficial Owner		Number				Class
A. Clinton Allen(5)			13,750				*
John K. McGillicuddy(5)			13,750				*
All directors and executive officers as a group (11 persons)(5)			2,202,906				4.72	%

*	Less than one percent
(1)	As of December 31, 2004, based on a Schedule 13G/ A filed by Mazama Capital Management, Inc. with the SEC on February 14, 2005, Mazama Capital Management, Inc. has sole voting power over 3,510,711 shares and sole dispositive power over 6,376,370 shares.
(2)	As of December 31, 2004, based on a Schedule 13G filed by TCW Group, Inc. with the SEC on February 14, 2005, TCW Group, Inc. has shared voting power over 2,133,387 shares and shared dispositive power over 2,761,879 shares.
(3)	As of July 11, 2005, based on a Schedule 13D filed by David Nierenberg with the SEC on July 12, 2005, David Nierenberg has sole voting power over 2,571,156 shares and sole dispositive power over 2,571,156 shares.
(4)	As of December 31, 2004, based on a Schedule 13G filed by Barclays Global Investors NA with the SEC on February 14, 2005, Barclays Global Investors NA has sole voting power over 2,047,892 shares and shared dispositive power over 2,235,355 shares.
(5)	Includes in some instances restricted stock over which the named individual has voting power but no investment power and shares that the named individuals have the right to acquire within 60 days from August 15, 2005 through the exercise of options. The amounts listed include shares under such options as follows: Mr. Therrien, 562,268; Mr. Grady, 245,076; Mr. Bellini, 65,251; Mr. Cassis, 213,578; Mr. Woodbury, 90,001; Mr. Emerick, 76,750; Mr. Khoury, 61,750; Mr. Martin, 34,750; Mr. Allen, 13,750; Mr. McGillicuddy, 13,750 and all directors and executive officers as a group, 1,232,252.
(6)	In February 2005 Mr. Frasso resigned as Senior Vice President of Global Operations of Brooks. Mr. Cassis resigned as Senior Vice President of Brooks effective August 26, 2005.

85

---

Table of Contents

	•	each person, including any partnership, syndicate, or other group, known to Helix management to be the beneficial owner of more than five percent of the outstanding shares of Helix common stock;
	•	each of Helix’s directors;
	•	Helix’s Chief Executive Officer during the fiscal year ended December 31, 2004, and Helix’s four other most highly compensated executive officers who were serving as executive officers of Helix on December 31, 2004, which is referred to in this joint proxy statement/ prospectus as the Named Executive Officers of Helix; and
	•	all of Helix’s executive officers and directors as a group.

			Shares Beneficially
			Owned
							Percent of
Beneficial Owner			Number				Class
5% Stockholders:
DePrince, Race & Zollo(1)				3,805,104				14.56	%
	201 South Orange Avenue
	Orlando, Florida 32801
T. Rowe Price Associates, Inc.(2)				2,502,600				9.57	%
	100 E. Pratt Street
	Baltimore, Maryland 21202
Babson Capital Management LLC(3)				2,021,475				7.73	%
	One Memorial Drive
	Boston, Massachusetts 02142
Putnam Investment Management LLC(4)				1,359,260				5.20	%
	Two Liberty Square
	Boston, Massachusetts 02109
Non-Employee Directors:
Gideon Argov(5)				2,000				**
Frank Gabron(5)				16,800				**
Robert H. Hayes(5)				13,900				**
Marvin G. Schorr(5)				108,800				**
Alfred Woollacott, III(5)				6,000				**
Mark S. Wrighton(5)				16,400				**
Named Executive Officers:
Robert J. Lepofsky*(5)(6)				400,011				1.52	%
James F. Gentilcore*(5)				49,580				**

86

---

Table of Contents

		Shares Beneficially
		Owned
						Percent of
Beneficial Owner		Number				Class
Jay Zager*(5)			1,407				**
Robert E. Anastasi(5)			121,164				**
Mark E. Jalbert(5)			34,289				**
All directors and executive officers as a group (11 persons)(5)(6)			770,351				2.91	%

	*	Effective January 1, 2005, Mr. Lepofsky retired as President and Chief Executive Officer of Helix and became the Chairman of the Board of Directors of Helix. On that date, Mr. Gentilcore became the President and Chief Executive Officer and a director of Helix. Mr. Zager resigned as Senior Vice President, Chief Financial Officer and Treasurer of Helix effective February 25, 2005.

**	Less than 1 percent of shares outstanding.

(1)	As of July 31, 2005, based on a Schedule 13G filed by DePrince, Race & Zollo, Inc. (“DRZ”) with the SEC on July 31, 2005, DRZ has sole dispositive and sole voting power with respect to all of these shares.
(2)	As of June 30, 2005, based on a Schedule 13 F-HR filed by T. Rowe Price Associates, Inc., (“T. Rowe Price”) with the SEC on August 15, 2005, T. Rowe Price has sole dispositive power with respect to all of these shares and sole voting power with respect to 874,400 of these shares.
(3)	As of June 30, 2005, based on a Schedule 13 F-HR filed by Babson Capital Management LLC (“Babson Capital”) with the SEC on July 27, 2005, Babson Capital has sole dispositive and sole voting power with respect to all of these shares.
(4)	As of June 30, 2005, based on Schedule 13 F-HR/A filed by Putnam Investment Management LLC (“Putnam Investment”) with the SEC on August 12, 2005, Putnam Investment has sole dispositive power with respect to all of these shares and sole voting power with respect to 382,800 of these shares.
(5)	Includes shares that each named individual has the right to acquire within 60 days from August 15, 2005 through the exercise of options. The amounts listed include shares under such options as follows: Mr. Gabron 4,000; Dr. Hayes, 2,000; Dr. Schorr, 4,000; Mr. Woollacott, 4,000; Dr. Wrighton 4,000; Mr. Lepofsky, 105,000; Mr. Anastasi, 118,750; Mr. Gentilcore, 45,250; Mr. Jalbert, 28,750 and all directors and executive officers as a group, 315,750. Also includes 1,945 shares for Mr. Lepofsky; 1,225 shares for Mr. Gentilcore; 1,407 shares for Mr. Zager; 2,414 shares for Mr. Anastasi; and 1,900 shares for Mr. Jalbert held in Helix’s 401(k) retirement savings plan.
(6)	Includes 40,000 shares held in a trust fund, with respect to which shares Mr. Lepofsky disclaims beneficial ownership.

87

---

Table of Contents

88

---

Table of Contents

89

---

Table of Contents

90

---

Table of Contents

91

---

Table of Contents

					Brooks				Helix				Adjustment				Pro Forma
					(In thousands)
ASSETS
	Current assets
		Cash and cash equivalents			$	162,796			$	11,980			$	—			$	174,776
		Marketable securities				138,841				17,920				—				156,761
		Accounts receivable, net				90,982				26,188				(45	)(n)			117,125
		Inventories				57,708				23,677				10,527	(k)			91,912
		Deferred income taxes				—				7,797				(7,797	)(d)			—
		Current assets from discontinued operations				156				—				—				156
		Prepaid expenses and other current assets				13,949				2,348				—				16,297
			Total current assets			464,432				89,910				2,685				557,027
	Property, plant and equipment, net					56,517				20,928				—				77,445
	Long-term marketable securities					48,087				—				—				48,087
	Goodwill					62,113				29,620				(29,620	)(a)			343,733
														281,620	(h)
	Intangible assets, net					4,565				13,396				(13,396	)(b)			86,165
														81,600	(g)
	Other assets					4,755				15,319				—				20,074
			Total assets		$	640,469			$	169,173			$	322,889			$	1,132,531
LIABILITIES, MINORITY INTERESTS AND STOCKHOLDERS’ EQUITY
	Current liabilities
		Current portion of long-term debt			$	12			$	—			$	—			$	12
		Accounts payable				37,019				6,196				(45	)(n)			43,170
		Deferred revenue				31,657				—				—				31,657
		Accrued warranty and retrofit costs				11,195				1,213				—				12,408
		Accrued compensation and benefits				15,024				1,197				—				16,221
		Accrued retirement benefit				—				3,326				—				3,326
		Accrued restructuring costs				9,802				—				—				9,802
		Accrued income taxes payable				16,477				4,002				—				20,479
		Current liabilities from discontinued operations				498				—				—				498
		Accrued expenses and other current liabilities				14,497				3,869				8,270	(e)			33,537
														6,901	(f)
			Total current liabilities			136,181				19,803				15,126				171,110
	Long-term debt					175,005				—				—				175,005
	Accrued long-term restructuring					10,304				—				—				10,304
	Retirement costs					—				7,653				—				7,653
	Deferred income taxes					—				406				(406	)(d)			—
	Other long-term liabilities					1,778				—				—				1,778
			Total liabilities			323,268				27,862				14,720				365,850
	Minority interests					991				—				—				991
	Stockholders’ equity
		Common stock				453				26,132				(26,132	)(c)			743
														290	(i)
		Additional paid-in capital				1,242,704				76,611				(76,611	)(c)			1,692,837
														444,089	(i)
														6,044	(j)
		Deferred compensation				(3,865	)			(130	)			130	(c)			(4,408	)
														(543	)(r)
		Accumulated other comprehensive income				12,772				794				(794	)(c)			12,772
		Retained earnings (accumulated deficit)				(935,854	)			37,904				(37,904	)(c)			(936,254	)
														(400	)(m)
			Total stockholders’ equity			316,210				141,311				308,169				765,690
			Total liabilities, minority interest and stockholders’ equity		$	640,469			$	169,173			$	322,889			$	1,132,531

92

---

Table of Contents

				Brooks				Helix				Adjustment				Pro Forma
				(In thousands, except per share amounts)
Net revenues				$	535,053			$	159,674			$	(498	)(q)		$	694,229
Cost of revenues					332,260				95,849				(498	)(q)			427,611
Gross profit					202,793				63,825				—				266,618
Operating expenses
	Research and development				65,821				10,826				73	(r)			76,720
	Selling, general and administrative				87,074				35,623				296	(r)			122,993
	Amortization of acquired intangible assets				3,663				—				12,657	(o)			16,320
	Restructuring and merger costs				5,356				—				—				5,356
		Total operating expenses			161,914				46,449				13,026				221,389
	Income from continuing operations				40,879				17,376				(13,026	)			45,229
	Joint venture income				—				3,508				—				3,508
	Interest income				4,984				1,065				—				6,049
	Interest expense				(9,492	)			—				—				(9,492	)
	Other expense, net				(911	)			—				—				(911	)
		Income from continuing operations before income taxes and minority interests			35,460				21,949				(13,026	)			44,383
	Income tax provision (benefit)				8,053				(5,562	)			5,697	(s)			8,188
	Income from continuing operations before minority interests				27,407				27,511				(18,723	)			36,195
	Minority interests in income of consolidated subsidiary				211				—				—				211
	Income from continuing operations			$	27,196			$	27,511			$	(18,723	)		$	35,984
Basic income per share from continuing operations				$	0.63			$	1.05							$	0.50
Diluted income per share from continuing operations				$	0.63			$	1.05							$	0.50
Shares used in computing earnings per share
	Basic				43,006				26,110								71,988
	Diluted				43,469				26,187								72,537

93

---

Table of Contents

				Brooks				Helix				Adjustment				Pro Forma
				(In thousands, except per share amounts)
Net revenues				$	360,447			$	115,716			$	(329	)(q)		$	475,834
Cost of revenues					234,436				69,006				(329	)(q)			302,533
													(580	)(l)
Gross profit					126,011				46,710				580				173,301
Operating expenses
	Research and development				48,075				8,949				28	(r)			57,052
	Selling, general and administrative				60,695				30,466				109	(r)			90,946
													(324	)(l)
	Amortization of acquired intangible assets				2,364				—				9,493	(o)			11,857
	Restructuring and merger costs				9,487				498				(498	)(p)			9,487
		Total operating expenses			120,621				39,913				8,808				169,342
	Income from continuing operations				5,390				6,797				(8,228	)			3,959
	Joint venture income				—				2,190				—				2,190
	Interest income				6,463				560				—				7,023
	Interest expense				(7,109	)			—				—				(7,109	)
	Other income, net				706				—				—				706
		Income from continuing operations before income taxes and minority interests			5,450				9,547				(8,228	)			6,769
	Income tax provision (benefit)				4,265				(5,515	)			5,219	(s)			3,969
	Income from continuing operations before minority interests				1,185				15,062				(13,447	)			2,800
	Minority interests in income of consolidated subsidiary				72				—				—				72
	Income from continuing operations			$	1,113			$	15,062			$	(13,447	)		$	2,728
Basic income per share from continuing operations				$	0.02			$	0.58							$	0.04
Diluted income per share from continuing operations				$	0.02			$	0.58							$	0.04
Shares used in computing earnings per share
	Basic				44,857				26,115								73,845
	Diluted				45,124				26,163								74,165

94

---

Table of Contents

1.	Basis of Pro Forma Presentation

95

---

Table of Contents

			Amount
			(In thousands)
Estimated fair value of Brooks common stock issued to Helix stockholders			$	444,379
Estimated fair value of assumed Helix options				6,044
Estimated direct transaction fees and expenses of Brooks				8,270
	Total preliminary estimated purchase price:		$	458,693

								First Year				Estimated Useful
				Amount				Charges (Credits)				Life
												(Years)
				(In thousands)
Net tangible assets				$	94,530			$	10,527	(1)			n/a
Identifiable intangible assets:
	Completed and core technology				58,300				9,110				5-10
	Trademarks and tradenames				4,700				783				6
	Customer and contract relationships				18,600				2,764				4-11
		Total identifiable intangible assets			81,600
Goodwill					281,620				—				n/a
Deferred stock-based compensation					543				369	(2)			4
In process research and development					400				400	(3)			n/a
		Total preliminary purchase price allocation		$	458,693

(1)	Reflects an increase in cost of goods sold of $10.5 million related to the revaluation of certain inventory to fair value. This charge is non-recurring and as such is not reflected in the unaudited pro forma condensed combined statements of operations.
(2)	Relates to compensation expense associated with unvested stock options assumed.
(3)	Reflects the estimated fair value of in-process research and development. This charge is non-recurring and as such is not reflected in the unaudited pro forma condensed combined statement of operations.

96

---

Table of Contents

	•	Helix historical operating margins
	•	Helix market share and growth
	•	Trends in technology
	•	The nature and expected timing of new product introductions by Helix and its competitors.

97

---

Table of Contents

2.	Pro Forma Adjustments

	(a)  To eliminate Helix’s historical goodwill
	(b)  To eliminate Helix’s historical intangible assets
	(c)  To eliminate Helix’s stockholders’ equity accounts
	(d)  To eliminate Helix’s historical deferred tax assets and liabilities
	(e)  To record Brooks’ estimated direct costs of the transaction
	(f)  To record Helix’s estimated direct costs of the transaction
	(g)  To record the fair value of Helix’s identifiable intangible assets
	(h)  To record goodwill
	(i)  To record the fair value of Brooks’ shares exchanged in the transaction
	(j)  To record the fair value of Helix’s stock options assumed

	(k)	To adjust Helix’s inventory to fair value less selling profit. This adjustment will result in an increase in cost of revenues upon the sale of the related inventory. This increase in costs is

98

---

Table of Contents

		non-recurring and accordingly is not reflected in the pro forma condensed combined statements of operations.

	(l)  To eliminate Helix’s historical amortization expense of its amortizable intangible assets

	(m)	To record the estimated fair value of in-process research and development

	(n)  To eliminate intercompany receivables and payables
	(o)  To record amortization of amortizable intangible assets
	(p)  To eliminate Helix’s historical expenses related to the merger with Brooks

	(q)	To eliminate intercompany sales and related cost of goods sold
	(r)	To record deferred stock-based compensation and related amortization associated with unvested Helix stock options assumed
	(s)	To adjust the Helix tax rate to an estimated effective tax rate, eliminate Helix’s historical reversal of a deferred tax valuation allowance, and to record income tax expense (benefit) associated with other pro forma adjustments

3.	Deferred Stock-Based Compensation.

4.	Pro Forma Earnings Per Share

99

---

Table of Contents

100

---

Table of Contents

	Certificate of Incorporation and Bylaws

101

---

Table of Contents

	Rights Agreement

	Indenture

	Delaware Law

102

---

Table of Contents

		Brooks Stockholder Rights		Helix Stockholder Rights
General:		The rights of Brooks stockholders are governed by Delaware law and Brooks’ certificate of incorporation and bylaws.		The rights of Helix stockholders are governed by Delaware law and Helix’s certificate of incorporation and bylaws.
Class of Common Stock:		Brooks has two classes of common stock authorized, Common Stock and Class A Common Stock, and one class of common stock outstanding, Common Stock.		Helix has only one class of common stock authorized and outstanding.
Preferred Stock:		Brooks has undesignated preferred stock and Series A Junior Participating Preferred Stock authorized. The Series A Junior Participating Preferred Stock is issuable upon exercise of outstanding stock purchase rights.		Helix has undesignated preferred stock authorized and no preferred stock outstanding or issuable upon exercise of stock purchase rights.
Authorized Capital Stock:		101,000,000 shares of stock (126,000,000 shares of stock if Brooks stockholders approve Brooks Proposal Number Two), of which 100,000,000 shares (125,000,000 shares of stock if Brooks stockholders approve Brooks Proposal Number Two) are designated as common stock		62,000,000 shares of stock, of which 60,000,000 shares are designated as common stock and 2,000,000 shares are designated as preferred stock.

103

---

Table of Contents

		Brooks Stockholder Rights		Helix Stockholder Rights
		and 1,000,000 shares are designated as preferred stock.
Number and Election of Directors:		Brooks’ bylaws provide that the board of directors determines the number of directors before each annual or special meeting of the stockholders. Currently, the number of directors is seven. Following the merger, there will be ten directors and one non-voting director emeritus. Three of the directors and the non-voting director emeritus will be selected by Helix from current members of Helix’s board of directors and seven directors will be the current directors of Brooks.		Helix’s bylaws provide that the number of directors will not be less than three or more than 15 as shall be determined by the board. Currently, the number of directors is eight.
Removal of Directors:		Under Brooks’ bylaws, a director may be removed from office only for cause by a vote of the holders of at least 80% of the voting stock outstanding or by a vote of a majority of the directors then in office, and only after reasonable notice and opportunity to be heard from the body proposing to remove the director.1		Under Helix’s bylaws, a director may be removed with or without cause by a majority of the stockholders of the outstanding shares entitled to vote.
Board Vacancies:		Under Brooks’ bylaws, vacancies on the board may be filled by a majority of directors, whether or not constituting a quorum. A director elected to fill a vacancy serves until the election of his successor.		Under Helix’s bylaws, vacancies on the board are filled by either the stockholders at any meeting of the stockholders, the board of directors at any meeting of the board of directors at which a quorum is present or by a majority of the directors then in office whether or not constituting a quorum. A director elected to fill a vacancy serves until a successor is duly elected and qualified.
Special Meetings:		Brooks’ bylaws provide that a special meeting of the stockholders may be called only by the president or the board of directors.		Helix’s bylaws provide that a special meeting of the stockholders may be called by the president or by the board of directors and will be so called at the written request of the registered holders of 20% or more of the stock of the corporation then outstanding and entitled to vote, which request must state the object of the meeting.
Notice of Stockholder Meetings:		Brooks’ bylaws require that written notice of meetings of stockholders, stating the place,		Helix’s bylaws require that written notice stating the time and place of the meeting be

104

---

Table of Contents

		Brooks Stockholder Rights		Helix Stockholder Rights
		date and hour, generally be given no less than ten or more than 60 days before the meeting to each stockholder entitled to vote at the meeting or entitled to notice of the meeting.		given at least ten days before the meeting to each stockholder entitled to vote at the meeting. The DGCL provides that notice of a stockholder meeting may not be given more than 60 days before the meeting.
Record Date:		Brooks’ bylaws provide that the record date must be no more than 60 days before the meeting.		The Helix bylaws provide that a record date may not be more than 50 days prior to the date of the corporate action to which it relates.
Stockholder Action by Written Consent:		Brooks’ certificate of incorporation and bylaws provide that the stockholders cannot act by written consent.		Helix’s bylaws provide that a meeting may be dispensed with if all of the stockholders who would have been entitled to vote consent to such action, which consent in writing will have the same force and effect as a vote taken at a meeting of the stockholders.2
Amendment of Bylaws:		Brooks’ certificate of incorporation and bylaws provide that the bylaws may be amended by a majority of the board of directors, except that the directors may not amend the bylaws in a manner which changes the stockholder voting requirements for any action, alters or abolishes any preferential right or rights of redemption applicable to a class of stock with shares outstanding, alters the amendment provision of the bylaws, or permits the board of directors to take any action which under the DGCL, the certificate of incorporation or the bylaws is required to be taken by the stockholders. The bylaws may also be amended by holders of a majority of all shares outstanding and entitled to vote, except that where the effect of the amendment would be to reduce any voting requirement otherwise required by the DGCL, the certificate of incorporation or another provision of the bylaws, such amendment requires the vote that would have been required by the DGCL, the certificate of incorporation or the bylaws.		Helix’s bylaws provide that the bylaws may be amended by the board of directors or by the stockholders.

105

---

Table of Contents

		Brooks Stockholder Rights		Helix Stockholder Rights
State Anti-Takeover Statute:		Brooks is subject to Section 203 of the DGCL.		Helix is subject to Section 203 of the DGCL.
Rights Agreement:		Brooks is a party to a rights agreement that generally would be triggered if a person beneficially acquires 15% or more of Brooks common stock.		Helix is not a party to a rights agreement.
Fiscal Year:		Brooks’ bylaws specify that Brooks’ fiscal year ends on September 30 of each year.		Helix’s bylaws specify that Helix’s fiscal year end is determined by Helix’s board of directors. Currently, Helix’s fiscal year ends on December 31 of each year.
Limitation of Liability of Directors and Officers:		Brooks’ certificate of incorporation provides that Brooks’ directors have no personal liability to either Brooks or its stockholders for monetary damages for breach of fiduciary duty as a director, except for liability (1) for breach of the director’s duty of loyalty to Brooks and its stockholders, (2) for acts or omissions not in good faith or which involve intentional misconduct or a knowing violation of the law, (3) under Section 174 of DGCL or (4) for any transaction from which the director derived an improper personal benefit.		Helix’s certificate of incorporation provides that Helix’s directors are not personally liable to Helix or its stockholders for monetary damages for breach of fiduciary duty as a director, except for liability(1) for any breach of the director’s duty of loyalty to Helix or its stockholders, (2) for acts or omissions not in good faith or which involve intentional misconduct or a knowing violation of law, (3) under Section 174 of the DGCL, or (4) for any transaction from which the director derived an improper personal benefit. The merger agreement requires that Brooks maintain these provisions in full force and effect until the sixth anniversary of the date on which the effective time of the merger occurs.
Indemnification of Directors and Officers:		Brooks’ certificate of incorporation and bylaws provide that Brooks may indemnify present and former directors and officers to the fullest extent of the law. Brooks’ bylaws also permit expenses to be advanced to indemnified persons in advance of a final disposition of proceedings against them if they undertake to repay the amounts advanced if there is a final determination that indemnification is not permitted.		Helix’s bylaws require indemnification of present and former directors and officers if the director or officer acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the best interest of Helix and, with respect to any criminal proceeding, had no reasonable cause to believe his or her conduct was unlawful. Helix’s bylaws also require that expenses be advanced to indemnified persons in advance of a final disposition of proceedings against them if the person undertakes to repay the amounts advanced if

106

---

Table of Contents

		Brooks Stockholder Rights		Helix Stockholder Rights
				there is a final determination that indemnification is not permitted. The merger agreement requires that Brooks maintain these provisions in full force and effect until the sixth anniversary of the date on which the effective time of the merger occurs.
Anti-“Greenmail” Provision:		Brooks’ certificate of incorporation provides that Brooks may not repurchase voting stock from a person or group who has beneficially owned more than 5% of Brooks’ outstanding voting stock for less than two years at a price in excess of the fair market value of that stock unless the repurchase is approved by holders of two- thirds of Brooks’ outstanding voting stock (other than stock held by the person or group from which the voting stock is proposed to be repurchased).		Helix’s certificate of incorporation does not contain a provision specifically targeted at “greenmail.”
Special Stockholder Voting Requirements:		Brooks’ certificate of incorporation provides that except as otherwise provided in Brooks’ certificate of incorporation, bylaws and any certificate of designations, any vote required by stockholders pursuant to the DGCL, other than the election of directors (which is not affected by this provision), is effective if recommended by a majority of the “Continuing Directors” (as defined in Brooks’ certificate of incorporation) and the vote of a majority of each class of stock outstanding and entitled to vote thereon; and if not recommended by a majority of the Continuing Directors, then by the vote of 80% of each class of stock outstanding and entitled to vote thereon.		The Helix certificate of incorporation does not contain an analogous voting requirement provision.

107

---

Table of Contents

	“The total number of shares of all classes of stock which the Corporation shall have authority to issue is (i) 125,000,000 shares of Common Stock, $.01 par value per share (the “Common Stock”), and (ii) 1,000,000 shares of Preferred Stock, $.01 par value per share (the “Preferred Stock).”

108

---

Table of Contents

109

---

Table of Contents

110

---

Table of Contents

111

---

Table of Contents

112

---

Table of Contents

113

---

Table of Contents

114

---

Table of Contents

	•	Annual Report on Form 10-K for the year ended September 30, 2004
	•	Proxy statement on Schedule 14A filed with the SEC on January 6, 2005
	•	Quarterly Reports on Form 10-Q for the quarters ended December 31, 2004, March 31, 2005 and June 30, 2005
	•	Current Reports on Form 8-K filed with the SEC on December 28, 2004, February 23, 2005, April 29, 2005, July 11, 2005 and August 24, 2005
	•	Description of Brooks common stock as set forth in the Registration Statement on Form 8-A filed on January 27, 1995, including any amendments or reports filed with the SEC for the purpose of updating such description
	•	Description of Brooks’ preferred stock purchase rights as set forth in the Registration Statement on Form 8-A filed on August 7, 1997, including any amendments or reports filed with the SEC for the purpose of updating such description

115

---

Table of Contents

	•	Annual Report on Form 10-K for the year ended December 31, 2004
	•	Proxy statement on Schedule 14A filed with the SEC on May 2, 2005
	•	Quarterly Reports on Form 10-Q for the quarters ended April 1, 2005 and July 1, 2005
	•	Current Reports on Form 8-K filed with the SEC on January 6, 2005, February 3, 2005, February 16, 2005, March 1, 2005 and July 11, 2005
	•	Amended Current Reports on Form 8-K/ A filed with the SEC on March 16, 2005 and April 28, 2005

116

---

Table of Contents

117

---

Table of Contents

A-1

---

Table of Contents

ARTICLE I THE MERGER					A-8
	1.1		The Merger		A-8
	1.2		Effective Time		A-9
	1.3		Closing		A-9
	1.4		Directors and Officers of the Surviving Corporation		A-9
	1.5		Effects of the Merger		A-9
	1.6		Conversion of Common Stock		A-9
	1.7		Company Options and Purchase Rights		A-10
	1.8		Closing of Company Transfer Books		A-10
	1.9		Exchange of Certificates		A-10
	1.10		No Liability		A-11
	1.11		Lost Certificates		A-11
	1.12		Withholding Rights		A-11
	1.13		Distributions with Respect to Unexchanged Shares		A-11
	1.14		Additional Matters		A-12
ARTICLE II REPRESENTATIONS AND WARRANTIES OF COMPANY					A-12
	2.1		Organization and Qualification		A-12
	2.2		Authority to Execute and Perform Agreement		A-13
	2.3		Capitalization and Title to Shares		A-13
	2.4		Company Subsidiaries		A-14
	2.5		SEC Reports		A-15
	2.6		Financial Statements		A-15
	2.7		Absence of Undisclosed Liabilities		A-16
	2.8		Absence of Adverse Changes		A-16
	2.9		Compliance with Laws		A-16
	2.10		Actions and Proceedings		A-17
	2.11		Contracts and Other Agreements		A-17
	2.12		Intellectual Property		A-17
	2.13		Assets		A-19
	2.14		Insurance		A-20
	2.15		Commercial Relationships		A-20
	2.16		Tax Matters		A-20
	2.17		Employee Benefit Plans		A-21
	2.18		Employee Relations		A-24
	2.19		Environmental Matters		A-24
	2.20		No Breach		A-25
	2.21		Board Approvals		A-25
	2.22		Financial Advisor		A-26
	2.23		Interested Party Transactions		A-26
	2.24		Information Supplied		A-26
ARTICLE III REPRESENTATIONS AND WARRANTIES OF PARENT AND SUB					A-26
	3.1		Organization and Qualification		A-27
	3.2		Authority to Execute and Perform Agreement		A-27
	3.3		Capitalization and Title to Shares		A-28
	3.4		Parent Subsidiaries		A-29
	3.5		SEC Reports		A-29

A-2

---

Table of Contents

	3.6		Financial Statements		A-30
	3.7		Absence of Undisclosed Liabilities		A-30
	3.8		Absence of Adverse Changes		A-30
	3.9		Compliance with Laws		A-31
	3.10		Actions and Proceedings		A-31
	3.11		Contracts and Other Agreements		A-31
	3.12		Intellectual Property		A-32
	3.13		Assets		A-33
	3.14		Insurance		A-34
	3.15		Commercial Relationships		A-34
	3.16		Tax Matters		A-34
	3.17		Employee Benefit Plans		A-35
	3.18		Employee Relations		A-38
	3.19		Environmental Matters		A-38
	3.20		No Breach		A-39
	3.21		Board Approvals		A-39
	3.22		Financial Advisor		A-39
	3.23		Interested Party Transactions		A-40
	3.24		Sub		A-40
	3.25		Information Supplied		A-40
ARTICLE IV COVENANTS AND AGREEMENTS					A-40
	4.1		Conduct of Company Business		A-40
	4.2		Conduct of Parent Business		A-43
	4.3		Corporate Examinations and Investigations		A-45
	4.4		Expenses		A-45
	4.5		Authorization from Others		A-46
	4.6		Further Assurances		A-46
	4.7		Preparation of Disclosure Documents; Stockholders Meetings		A-46
	4.8		Public Announcements		A-48
	4.9		Affiliate Letters		A-48
	4.10		Nasdaq Listings		A-48
	4.11		No Solicitation		A-48
	4.12		Regulatory Filings		A-50
	4.13		Notification of Certain Matters		A-50
	4.14		Registration of Certain Shares		A-50
	4.15		Employee Matters		A-51
	4.16		Board Membership and Officers		A-51
	4.17		Indemnification		A-52
	4.18		Section 16 Approval		A-52
	4.19		Participation in Certain Actions and Proceedings		A-52
	4.20		Tax-Free Reorganization		A-53
	4.21		No Acquisition of Common Stock		A-53
	4.22		FIRPTA Certificate		A-53
ARTICLE V CONDITIONS PRECEDENT TO THE OBLIGATIONS OF EACH PARTY TO CONSUMMATE THE MERGER					A-53
	5.1		Stockholder Approval		A-53
	5.2		Registration Statement		A-53
	5.3		Absence of Order		A-53

A-3

---

Table of Contents

	5.4		Regulatory Approvals		A-53
	5.5		Pending Litigation		A-53
	5.6		HSR Act		A-54
	5.7		Nasdaq		A-54
ARTICLE VI CONDITIONS PRECEDENT TO THE OBLIGATIONS OF PARENT AND SUB TO CONSUMMATE THE MERGER					A-54
	6.1		Representations, Warranties and Covenants		A-54
	6.2		Corporate Certificates		A-54
	6.3		Secretary’s Certificate		A-54
	6.4		Tax Opinion		A-54
ARTICLE VII CONDITIONS PRECEDENT TO THE OBLIGATION OF COMPANY TO CONSUMMATE THE MERGER					A-55
	7.1		Representations, Warranties and Covenants		A-55
	7.2		Corporate Certificates		A-55
	7.3		Secretary’s Certificate		A-55
	7.4		Tax Opinion		A-55
ARTICLE VIII TERMINATION, AMENDMENT AND WAIVER					A-55
	8.1		Termination		A-55
	8.2		Effect of Termination		A-57
	8.3		Amendment		A-58
	8.4		Waiver		A-58
ARTICLE IX MISCELLANEOUS					A-58
	9.1		No Survival		A-58
	9.2		Notices		A-58
	9.3		Entire Agreement		A-59
	9.4		Governing Law		A-59
	9.5		Binding Effect; No Assignment; No Third-Party Beneficiaries		A-59
	9.6		Section Headings		A-60
	9.7		Counterparts		A-60
	9.8		Severability		A-60
	9.9		Submission to Jurisdiction; Waiver		A-60
	9.10		Enforcement		A-60
	9.11		Rules of Construction		A-60
	9.12		Waiver of Jury Trial		A-61

A-4

---

Table of Contents

		Section
“Affiliate Letters”		4.9
“Agreement”		Preamble
“Certificate of Merger”		1.2(a)
“Certificates”		1.9(a)
“Closing Date”		1.3
“Closing”		1.3
“Code”		Recitals
“Company”		Preamble
“Company 10-K”		2.5(a)
“Company 10-Q”		2.6(a)
“Company Acquisition Proposal”		4.11
“Company Adverse Recommendation Change”		4.11(c)
“Company Agreements”		2.11
“Company Balance Sheet”		2.7
“Company Board of Directors”		Recitals
“Company Common Stock”		1.6(a)(i)
“Company Disclosure Schedule”		Article II
“Company Foreign Plan”		2.17(l)
“Company ERISA Affiliate”		2.17(a)
“Company Joint Venture”		2.4(c)
“Company Leased Real Property”		2.13(b)
“Company Material Adverse Effect”		2.1(a)
“Company Options”		1.7(a)
“Company Permits”		2.9(b)
“Company Plans”		2.17(a)
“Company Preferred Stock”		2.3(c)
“Company Real Property”		2.13
“Company Real Property Leases”		2.13(b)
“Company Real Property”		2.13(b)
“Company SEC Reports”		2.5(a)
“Company Stock Option Plans”		1.7(a)
“Company Stockholder Approval”		4.7(b)
“Company Stockholders Meeting”		4.7(b)
“Company Subsidiary”		2.4(a)
“Company Superior Proposal”		4.11(b)
“Confidentiality Agreement”		4.3
“Continuation Period”		4.15(a)
“Continuing Employees”		4.15(a)
“DGCL”		Recitals
“DOJ”		4.12
“Effective Time”		1.2(a)
“Environmental Laws”		2.19(a)

A-5

---

Table of Contents

		Section
“ERISA”		2.17(a)
“Exchange Act”		2.5(a)
“Exchange Agent”		1.9(a)
“Exchange Ratio”		1.6(a)(i)
“FTC”		4.12
“GAAP”		2.6(a)
“Hazardous Substance”		2.19(a)(ii)
“HSR Act”		2.20
“IRS”		2.17(b)
“knowledge of Parent” or “to the Parent’s knowledge”		3.3(e)
“knowledge of the Company” or “to the Company’s knowledge”		2.3(e)
“Laws”		2.9(a)
“Merger Consideration”		1.6(a)(iii)
“Merger”		1.1(a)
“Morgan Stanley”		2.22(a)
“Parent”		Preamble
“Parent 10-K”		3.5(a)
“Parent 10-Q”		3.6(a)
“Parent Adverse Recommendation Change”		4.7(c)
“Parent Agreements”		3.11
“Parent Balance Sheet”		3.7
“Parent Board of Directors”		Recitals
“Parent Common Stock”		1.6(a)(i)
“Parent Foreign Plan”		3.17(l)
“Parent Disclosure Schedule”		Article III
“Parent ERISA Affiliate”		3.17(a)
“Parent Expenses”		8.2(b)
“Parent Joint Venture”		3.4(c)
“Parent Leased Real Property”		3.13(c)
“Parent Material Adverse Effect”		3.1(a)
“Parent Options”		3.3(b)
“Parent Owned Real Property”		3.13(b)
“Parent Plans”		3.17(a)
“Parent Preferred Stock”		3.3(c)
“Parent Real Property Leases”		3.13(c)
“Parent Real Property”		3.13(c)
“Parent Rights”		3.3(c)
“Parent SEC Reports”		3.5(a)
“Parent Stockholder Approval”		4.7(c)
“Parent Stockholders Meeting”		4.7(c)
“Parent Subsidiary”		3.4(a)
“Permitted Encumbrances”		2.13(a)
“Proprietary Rights”		2.12(a)
“Joint Proxy Statement/ Prospectus”		4.7(a)

A-6

---

Table of Contents

		Section
“Registration Statement”		4.7(a)
“Regulation M-A Filing”		2.24
“Representatives”		4.11(a)
“Restraints”		8.1(c)
“Secretary of State”		1.2(a)
“Securities Act”		2.5(b)
“Sub”		Preamble
“Surviving Corporation”		1.1(a)
“Tax Return”		2.16(a)
“Tax”, “Taxes” and “Taxable”		2.16(a)
“Termination Date”		8.1(b)
“Termination Fee”		8.2(b)

A-7

---

Table of Contents

A-8

---

Table of Contents

	(i) Subject to payment of cash in lieu of fractional shares as provided below, each share of Company common stock, $1.00 par value per share (“Company Common Stock”), outstanding immediately prior to the Effective Time, other than shares held by Company as treasury stock and shares held by Parent or Sub, will be cancelled and extinguished and automatically converted into and become the right to receive 1.11 (the “Exchange Ratio”) shares of Parent common stock, $.01 par value per share (“Parent Common Stock”), and the associated Parent Rights (as defined in Section 3.3(c)).
	(ii) If prior to the Effective Time there is a change in the number of issued and outstanding shares of Parent Common Stock or Company Common Stock as the result of reclassification, subdivision, recapitalization, stock split (including reverse stock split), stock dividend or similar transactions, the Exchange Ratio shall be equitably adjusted to give effect to such event to provide the stockholders of Company Common Stock the same economic effect as contemplated by this Agreement prior to such event.
	(iii) The shares of Parent Common Stock payable pursuant to this Section 1.6(a), together with cash payments in lieu of fractional shares pursuant to Section 1.6(b), are referred to collectively as the “Merger Consideration.”

A-9

---

Table of Contents

A-10

---

Table of Contents

A-11

---

Table of Contents

A-12

---

Table of Contents

A-13

---

Table of Contents

A-14

---

Table of Contents

A-15

---

Table of Contents

A-16

---

Table of Contents

A-17

---

Table of Contents

	(i) to the knowledge of Company, (A) the business conducted by Company and the Company Subsidiaries does not infringe upon the Proprietary Rights of any third party, and (B) none of Company or any the Company Subsidiaries has infringed upon, misappropriated or otherwise violated the Proprietary Rights of any third party;
	(ii) Company has never received any written charge, complaint, claim, demand or notice alleging any such infringement, misappropriation, or violation (including any claim that Company or a Company Subsidiary must license or refrain from using any Proprietary Rights of any third party);
	(iii) no claims are pending or, to the knowledge of Company threatened, that Company or any of its Subsidiaries is infringing (including with respect to the manufacture, use or sale by Company or any of its Subsidiaries of their respective commercial products and services) the Proprietary Rights of any person; and
	(iv) as of the date of this Agreement, to the knowledge of Company, no person or entity has infringed upon, misappropriated or otherwise violated the Proprietary Rights of Company or any of its Subsidiaries.

A-18

---

Table of Contents

A-19

---

Table of Contents

A-20

---

Table of Contents

A-21

---

Table of Contents

A-22

---

Table of Contents

	(i) multi-employer plan as defined in Section 3(37) or Section 4001(a)(3) of ERISA,
	(ii) multiple employer plan as defined in Section 413(c) of the Code, or any plan that has two or more contributing sponsors at least two of whom are not under common control, within the meaning of Section 4063(a) of ERISA,
	(iii) welfare benefit fund within the meaning of Section 419(e) of the Code, or
	(iv) voluntary employees’ beneficiary association, within the meaning of Section 501(c)(9) of the Code.

A-23

---

Table of Contents

	(i) Company and the Company Subsidiaries are, and have been, in compliance in all respects with all Laws relating to (A) releases or threatened releases of Hazardous Substances (as defined

A-24

---

Table of Contents

	below), (B) pollution or protection of public health or the environment or worker safety or health or (C) the manufacture, handling, transport, use, treatment, storage, or disposal of Hazardous Substances (“Environmental Laws”);
	(ii) there has been no release or threatened release of any pollutant, petroleum or any fraction thereof, contaminant or toxic or hazardous material, substance or waste (each a “Hazardous Substance”) on, upon, into or from any site currently or heretofore owned, leased or otherwise used by Company, any Company Subsidiary or any predecessor of Company or any Company Subsidiary;
	(iii) there have been no Hazardous Substances generated by Company, any Company Subsidiary or any predecessor of Company or any Company Subsidiary that have been disposed of or come to rest at any site that has been included in any published U.S. federal, state or local “superfund” site list or any other similar list of hazardous or toxic waste sites published by any governmental entity in the United States; and
	(iv) there are no underground storage tanks located on, no PCBs (polychlorinated biphenyls) or PCB-containing equipment used or stored on, and no hazardous waste as defined by the Resource Conservation and Recovery Act stored on, any site owned or operated by Company, any Company Subsidiary or any predecessor of Company or any Company Subsidiary, except for the storage of hazardous waste in compliance with Environmental Laws.

A-25

---

Table of Contents

A-26

---

Table of Contents

A-27

---

Table of Contents

A-28

---

Table of Contents

A-29

---

Table of Contents

A-30

---

Table of Contents

A-31

---

Table of Contents

	(i) to the knowledge of Parent, (A) the business conducted by Parent and the Parent Subsidiaries does not infringe upon the Proprietary Rights of any third party, and (B) none of Parent or any the Parent Subsidiaries has infringed upon, misappropriated or otherwise violated the Proprietary Rights of any third party;
	(ii) Parent has never received any written charge, complaint, claim, demand or notice alleging any such infringement, misappropriation, or violation (including any claim that Parent or a Parent Subsidiary must license or refrain from using any Proprietary Rights of any third party);

A-32

---

Table of Contents

	(iii) no claims are pending or, to the knowledge of Parent threatened, that Parent or any of its Subsidiaries is infringing (including with respect to the manufacture, use or sale by Parent or any of its Subsidiaries of their respective commercial products and services) the Proprietary Rights of any person; and
	(iv) as of the date of this Agreement, to the knowledge of Parent, no person or entity has infringed upon, misappropriated or otherwise violated the Proprietary Rights of Parent or any of its Subsidiaries.

A-33

---

Table of Contents

A-34

---

Table of Contents

A-35

---

Table of Contents

A-36

---

Table of Contents

	(i) multi-employer plan as defined in Section 3(37) or Section 4001(a)(3) of ERISA,
	(ii) multiple employer plan as defined in Section 413(c) of the Code, or any plan that has two or more contributing sponsors at least two of whom are not under common control, within the meaning of Section 4063(a) of ERISA,
	(iii) welfare benefit fund within the meaning of Section 419(e) of the Code, or
	(iv) voluntary employees’ beneficiary association, within the meaning of Section 501(c)(9) of the Code.

A-37

---

Table of Contents

	(i) Parent and the Parent Subsidiaries are, and have been, in compliance in all respects with all Environmental Laws;
	(ii) there has been no release or threatened release of any Hazardous Substance on, upon, into or from any site currently or heretofore owned, leased or otherwise used by Parent, any Parent Subsidiary or any predecessor of Parent or any Parent Subsidiary;
	(iii) there have been no Hazardous Substances generated by Parent, any Parent Subsidiary or any predecessor of Parent or any Parent Subsidiary that have been disposed of or come to rest at any site that has been included in any published U.S. federal, state or local “superfund” site list or any other similar list of hazardous or toxic waste sites published by any governmental entity in the United States; and
	(iv) there are no underground storage tanks located on, no PCBs (polychlorinated biphenyls) or PCB-containing equipment used or stored on, and no hazardous waste as defined by the Resource

A-38

---

Table of Contents

	Conservation and Recovery Act stored on, any site owned or operated by Parent, any Parent Subsidiary or any predecessor of Parent or any Parent Subsidiary, except for the storage of hazardous waste in compliance with Environmental Laws.

A-39

---

Table of Contents

	(a) Affirmative Covenants Pending Closing. Company shall and shall cause the Company Subsidiaries to:

	(i) Preservation of Personnel. Use reasonable commercial efforts to preserve intact and keep available the services of present employees of Company and the Company Subsidiaries as a group;
	(ii) Insurance. Use reasonable commercial efforts to keep in effect casualty, public liability, worker’s compensation and other insurance policies in coverage amounts substantially similar to those in effect at the date of this Agreement;
	(iii) Preservation of the Business; Maintenance of Properties, Contracts. Use reasonable commercial efforts to preserve the business of Company and to develop, advertise, promote, market and sell Company’s products, and use reasonable commercial efforts to keep Company’s properties substantially intact, to preserve its goodwill and business, to maintain all physical properties in such operating condition as will permit the conduct of Company’s business on a basis consistent with past practice, and to perform and comply in all material respects with the terms of the contracts referred to in Section 2.11.
	(iv) Intellectual Property Rights. Use its reasonable best efforts to maintain, preserve and protect Company’s Proprietary Rights;

A-40

---

Table of Contents

	(v) Ordinary Course of Business. Operate Company’s business in the ordinary course consistent with past practices;
	(vi) Company Options. Take all reasonable actions necessary with respect to Company Options to effectuate the terms of this Agreement, provided, however, that Parent shall have the right to approve any agreements to modify material terms of the underlying instruments; and

	(b) Negative Covenants Pending Closing. Company shall not and shall cause the Company Subsidiaries not to:

	(i) Disposition of Assets. Sell or transfer, or mortgage, pledge, lease, license or otherwise encumber any of its assets, including its Proprietary Rights, other than sales or transfers of inventory in the ordinary course of business and other sales and transfers in amounts not exceeding, in the aggregate, $250,0000;
	(ii) Liabilities. (A) Incur any indebtedness for borrowed money in excess of $250,000 in the aggregate or (B) incur any obligation or liability or enter into any contract or commitment involving potential payments to or by Company or any Company Subsidiary in an amount aggregating in excess of $250,000 other than in the ordinary course of business consistent with past practice;
	(iii) Compensation. Increase or agree to increase the compensation payable to any officer, director, employee, agent or consultant, or enter into any employment, severance, retention or other agreement or arrangement with any officer, director, employee, agent or consultant of Company or a Company Subsidiary, or adopt, or increase the benefits (including fringe benefits) under, any employee benefit plan or otherwise, except (A), in each case, as required by law or in accordance with existing agreements disclosed in the Company Disclosure Schedule or filed as an exhibit to a Company SEC Report and (B), in the case of compensation for employees, agents or consultants who are not executive officers or directors, in the ordinary course of business consistent with past practice; or make any loans to any of its directors, officers or employees, agents or consultants, or make any change in its existing borrowing or lending arrangements for or on behalf of any such persons pursuant to an employee benefit plan or otherwise;
	(iv) Capital Stock. Make any change in the number of shares of Company’s capital stock authorized, issued or outstanding or grant or accelerate the exercisability of any option, warrant or other right to purchase, or convert any obligation into, shares of its capital stock, declare or pay any dividend (other than in the ordinary course of business consistent with past practice, including with respect to timing and amount) or other distribution with respect to any shares of its capital stock, reclassify, combine, split or subdivide any of its capital stock or issue or authorize any other securities in respect of, in lieu of or in substitution for shares of its capital stock, sell or transfer any shares of its capital stock, or redeem or otherwise repurchase any shares of its capital stock, except upon the exercise of convertible securities outstanding on July 6, 2005 and disclosed herein or in connection with the grants of Company Options to purchase not more than 75,000 shares of Company Common Stock after July 6, 2005 with exercise prices equal to the trading price of Company Common Stock on the date of grant in the ordinary course of business consistent with past practice;
	(v) Charter, By-laws, Directors and Officers. Cause, permit or propose any amendment to the Certificate of Incorporation or By-laws of Company or elect or appoint any new directors or officers;
	(vi) Acquisitions. Make, or permit to be made, any acquisition, lease, investment, or capital contribution in excess of $1,000,000 outside the ordinary course of business consistent with past practice;
	(vii) Capital Expenditures. Authorize any single capital expenditure in excess of $250,000 or capital expenditures which in the aggregate exceed $2,500,000;

A-41

---

Table of Contents

	(viii) Investments. Except for cash management activities in the ordinary course of business, purchase any securities or make any investment, either by purchase of securities, contributions to capital, asset transfers, or purchase of any assets (including any interests), in any person (including joint ventures), or otherwise acquire in any way direct or indirect control over any person, or agree to do any of the foregoing, in one transaction or a series of related transactions;
	(ix) Accounting Policies. Except as may be required as a result of a change in law or in GAAP, change any of the accounting practices or principles used by it;
	(x) Tax Treatment. Take, or permit any of the Company Subsidiaries to take, any action that would prevent the Merger from qualifying as a reorganization within the meaning of Section 368(a) of the Code;
	(xi) Taxes. Change any material Tax election or settle or compromise any material federal, state, local or foreign Tax liability, change any annual tax accounting period, change any method of Tax accounting, enter into any closing agreement relating to any material Tax or surrender any right to claim a material Tax refund;
	(xii) Legal. Commence, settle or compromise any pending or threatened suit, action or claim which (A) is material to Company and the Company Subsidiaries or which relates to the transactions contemplated hereby, (B) would involve material restrictions on the business activities of Company or any Company Subsidiary, or (C) would involve the issuance of Company securities;
	(xiii) Extraordinary Transactions. Adopt a plan of complete or partial liquidation, dissolution, merger, consolidation, restructuring, recapitalization or other reorganization of Company or any of the Company Subsidiaries (other than the Merger);
	(xiv) Payment of Indebtedness. Pay, discharge or satisfy any material claims, liabilities or obligations (absolute, accrued, asserted or unasserted, contingent or otherwise), other than the payment, discharge or satisfaction, in the ordinary course of business and consistent with past practice, of liabilities reflected or reserved against in the balance sheet included in the Company 10-Q or incurred in the ordinary course of business;
	(xv) WARN Act. Effectuate a “plant closing” or “mass layoff,” as those terms are defined in the Worker Adjustment and Retraining Notification Act of 1988 or effectuate any similar action under any foreign law;
	(xvi) New Agreements/ Amendments. Enter into, terminate or materially modify, or permit a Company Subsidiary to enter into, terminate or materially modify, any Company Agreement other than a contract or agreement that is a Company Agreement solely because it is described in Item 601(b)(10)(iii) of Regulation S-K;
	(xvii) Intellectual Property Rights. Fail to pay any fee, take any action or make any filing reasonably necessary to maintain material Proprietary Rights of Company other than licenses of software to customers in the ordinary course of business consistent with past practice;
	(xviii) Confidentiality and Standstill Agreements. Modify, amend or terminate, or waive, release or assign any material rights or claims with respect to any confidentiality or standstill agreement to which Company or any Company Subsidiary is a party and which relates to a business combination involving Company or any Company Subsidiary;
	(xix) Changes to Takeover Defenses. Amend, modify or waive any of Company’s existing takeover defenses or take any action to render any state takeover statutes inapplicable to any transaction other than the transactions contemplated by this Agreement;
	(xx) Obligations. Obligate itself to do any of the foregoing.

A-42

---

Table of Contents

	(c) Control of Company’s Business. Nothing contained in this Agreement shall give Parent, directly or indirectly, the right to control or direct Company’s operations prior to the Effective Time. Prior to the Effective Time, Company shall exercise, consistent with the terms and conditions of this Agreement, complete control and supervision over its operations.

	(a) Affirmative Covenants Pending Closing. Parent shall and shall cause the Parent Subsidiaries to:

	(i) Preservation of Personnel. Use reasonable commercial efforts to preserve intact and keep available the services of present employees of Parent and the Parent Subsidiaries as a group;
	(ii) Insurance. Use reasonable commercial efforts to keep in effect casualty, public liability, worker’s compensation and other insurance policies in coverage amounts substantially similar to those in effect at the date of this Agreement;
	(iii) Preservation of the Business; Maintenance of Properties, Contracts. Use reasonable commercial efforts to preserve the business of Parent and to develop, advertise, promote, market and sell Parent’s products, and use reasonable commercial efforts to keep Parent’s properties substantially intact, to preserve its goodwill and business, to maintain all physical properties in such operating condition as will permit the conduct of Parent’s business on a basis consistent with past practice, and to perform and comply in all material respects with the terms of the contracts referred to in Section 3.11.
	(iv) Intellectual Property Rights. Use its reasonable best efforts to maintain, preserve and protect Parent’s Proprietary Rights;
	(v) Ordinary Course of Business. Operate Parent’s business in the ordinary course consistent with past practices;

	(b) Negative Covenants Pending Closing. Parent shall not and shall cause the Parent Subsidiaries not to:

	(i) Disposition of Assets. Sell or transfer, or mortgage, pledge, lease, license or otherwise encumber any of its assets, including its Proprietary Rights, other than sales or transfers of inventory in the ordinary course of business and other sales and transfers in amounts not exceeding, in the aggregate, $1,000,000;
	(ii) Liabilities. (A) Incur any indebtedness for borrowed money in excess of $500,000 in the aggregate or (B) incur any obligation or liability or enter into any contract or commitment involving potential payments to or by Parent or any Parent Subsidiary in an amount aggregating in excess of $2,000,000 other than in the ordinary course of business consistent with past practice;
	(iii) Compensation. Increase or agree to increase the compensation payable to any officer, director, employee, agent or consultant, or enter into any employment, severance, retention or other agreement or arrangement with any officer, director, employee, agent or consultant of Parent or a Parent Subsidiary, or adopt, or increase the benefits (including fringe benefits) under, any employee benefit plan or otherwise, except (A), in each case, as required by law or in accordance with existing agreements disclosed in the Parent Disclosure Schedule or filed as an exhibit to a Parent SEC Report and (B), in the case of compensation for employees, agents or consultants who are not executive officers or directors, in the ordinary course of business consistent with past practice; or make any loans to any of its directors, officers or employees, agents or consultants, or make any change in its existing borrowing or lending arrangements for or on behalf of any such persons pursuant to an employee benefit plan or otherwise;

A-43

---

Table of Contents

	(iv) Capital Stock. Make any change in the number of shares of Parent’s capital stock authorized, issued or outstanding or grant or accelerate the exercisability of any option, warrant or other right to purchase, or convert any obligation into, shares of its capital stock, declare or pay any dividend or other distribution with respect to any shares of its capital stock, reclassify, combine, split or subdivide any of its capital stock or issue or authorize any other securities in respect of, in lieu of or in substitution for shares of its capital stock, sell or transfer any shares of its capital stock, or redeem or otherwise repurchase any shares of its capital stock, except upon the exercise of convertible securities outstanding on July 6, 2005 and disclosed herein or in connection with the grant of Parent Options with exercises prices equal to the trading price of Company Common Stock on the date of grant or the grant of restricted Parent Common Stock for compensatory purposes, in either case in the ordinary course of business consistent with past practice;
	(v) Charter, By-laws, Directors and Officers. Cause, permit or propose any amendment to the Certificate of Incorporation or By-laws of Parent or elect or appoint any new directors or officers;
	(vi) Acquisitions. Make, or permit to be made, any acquisition, lease, investment, or capital contribution in excess of $2,000,000 outside the ordinary course of business consistent with past practice;
	(vii) Capital Expenditures. Authorize any single capital expenditure in excess of $1,000,000 or capital expenditures which in the aggregate exceed $5,000,000;
	(viii) Investments. Except for cash management activities in the ordinary course of business, purchase any securities or make any investment, either by purchase of securities, contributions to capital, asset transfers, or purchase of any assets (including any interests), in any person (including joint ventures), or otherwise acquire in any way direct or indirect control over any person, or agree to do any of the foregoing, in one transaction or a series of related transactions;
	(ix) Accounting Policies. Except as may be required as a result of a change in law or in GAAP, change any of the accounting practices or principles used by it;
	(x) Tax Treatment. Take, or permit any of the Parent Subsidiaries to take, any action that would prevent the Merger from qualifying as a reorganization within the meaning of Section 368(a) of the Code;
	(xi) Taxes. Change any material Tax election or settle or compromise any material federal, state, local or foreign Tax liability, change any annual tax accounting period, change any method of Tax accounting, enter into any closing agreement relating to any material Tax, or surrender any right to claim a material Tax refund;
	(xii) Legal. Commence, settle or compromise any pending or threatened suit, action or claim which (A) is material to Parent and the Parent Subsidiaries or which relates to the transactions contemplated hereby, (B) would involve material restrictions on the business activities of Parent or any Parent Subsidiary, or (C) would involve the issuance of Parent securities;
	(xiii) Extraordinary Transactions. Adopt a plan of complete or partial liquidation, dissolution, merger, consolidation, restructuring, recapitalization or other reorganization of Parent or any of the Parent Subsidiaries (other than the Merger);
	(xiv) Payment of Indebtedness. Pay, discharge or satisfy any material claims, liabilities or obligations (absolute, accrued, asserted or unasserted, contingent or otherwise), other than the payment, discharge or satisfaction, in the ordinary course of business and consistent with past practice, of liabilities reflected or reserved against in the balance sheet included in the Parent 10-Q or incurred in the ordinary course of business;

A-44

---

Table of Contents

	(xv) WARN Act. Effectuate a “plant closing” or “mass layoff,” as those terms are defined in the Worker Adjustment and Retraining Notification Act of 1988 or effectuate any similar action under any foreign law;
	(xvi) New Agreements/ Amendments. Enter into, terminate or materially modify, or permit a Parent Subsidiary to enter into, terminate or materially modify, any Parent Agreement other than a contract or agreement that is a Parent Agreement solely because it is described in Item 601(b)(10)(iii) of Regulation S-K;
	(xvii) Intellectual Property Rights. Fail to pay any fee, take any action or make any filing reasonably necessary to maintain material Proprietary Rights of Parent other than licenses of software to customers in the ordinary course of business consistent with past practice;
	(xviii) Changes to Takeover Defenses. Amend, modify or waive any of Parent’s existing takeover defenses or take any action to render any state takeover statutes inapplicable to any transaction other than the transactions contemplated by this Agreement;
	(xix) Obligations. Obligate itself to do any of the foregoing.

	(c) Control of Parent’s Business. Nothing contained in this Agreement shall give Company, directly or indirectly, the right to control or direct Parent’s operations prior to the Effective Time. Prior to the Effective Time, Parent shall exercise, consistent with the terms and conditions of this Agreement, complete control and supervision over its operations.

A-45

---

Table of Contents

A-46

---

Table of Contents

A-47

---

Table of Contents

A-48

---

Table of Contents

A-49

---

Table of Contents

A-50

---

Table of Contents

A-51

---

Table of Contents

A-52

---

Table of Contents

A-53

---

Table of Contents

A-54

---

Table of Contents

	(a) By mutual written consent of Parent and Company authorized by the Parent Board of Directors and the Company Board of Directors; or
	(b) By either Parent or Company if the Merger has not been consummated by February 15, 2006 (the “Termination Date”); provided, however, that the right to terminate this Agreement pursuant to this Section 8.1(b) shall not be available to any party whose action or failure to fulfill any

A-55

---

Table of Contents

	obligation under this Agreement has been the principal cause of, or resulted in, the failure of the Merger to be consummated by such date; or
	(c) By either Parent or Company if a court of competent jurisdiction or other governmental entity shall have issued an order, decree or ruling or taken any other action, and such order, decree or ruling or other action shall have become final and nonappealable, or there shall exist any statute, rule or regulation, in each case restraining, enjoining or otherwise prohibiting (collectively, “Restraints”) the consummation of any of the transactions contemplated hereby; provided, however, that the party seeking to terminate this Agreement pursuant to this Section 8.1(c) has used all reasonable efforts to prevent the entry of and to remove such Restraints; or
	(d) By Parent if there has been a breach of, or inaccuracy in, any representation, warranty, covenant or agreement of Company set forth in this Agreement, which breach or inaccuracy has resulted or is reasonably likely to result in any condition set forth in Article VI not being satisfied (and such breach or inaccuracy has not been cured or such condition has not been satisfied within thirty (30) days after the receipt of notice thereof or such breach or inaccuracy is not reasonably capable of being cured or such condition is not reasonably capable of being satisfied within such period); or
	(e) By Company if there has been a breach of, or inaccuracy in, any representation, warranty, covenant or agreement of Parent or Sub set forth in this Agreement, which breach or inaccuracy has resulted or is reasonably likely to result in any condition set forth in Article VII not being satisfied (and such breach or inaccuracy has not been cured or such condition has not been satisfied within thirty (30) days after the receipt of notice thereof or such breach or inaccuracy is not reasonably capable of being cured or such condition is not reasonably capable of being satisfied within such period); or
	(f) By Parent, if (i) the Company Board of Directors shall have (A) withdrawn, modified or changed its approval or recommendation of this Agreement or the Merger, or publicly announced its intention to do so, or failed to recommend this Agreement or the Merger, (B) approved or recommended to Company’s stockholders any proposal other than by Parent or Sub in respect of any Company Acquisition Proposal, or entered into or publicly announced its intention to enter into any agreement or agreement in principle in respect of any Company Acquisition Proposal, (C) resolved or publicly proposed to any of the foregoing or (D) failed to recommend against, or taken a neutral position with respect to, a tender or exchange offer related to a Company Acquisition Proposal in any position taken pursuant to Rules 14d-9 and 14e-2 under the Exchange Act or (ii) Company shall have violated or breached in any material respect its obligations under Section 4.11; or
	(g) By Company, if (i) the Parent Board of Directors shall have (A) withdrawn, modified or changed its approval or recommendation that Parent stockholders approve the issuance of shares of Parent Common Stock pursuant to this Agreement, or publicly announced its intention to do so, or failed to recommend that Parent stockholders approve the issuance of shares of Parent Common Stock pursuant to this Agreement or (B) resolved or publicly proposed to any of the foregoing; or
	(h) By either Parent or Company, if upon a vote at a duly held meeting to obtain Company Stockholder Approval, Company Stockholder Approval is not obtained or if upon a vote at a duly held meeting to obtain Parent Stockholder Approval, Parent Stockholder Approval is not obtained.
	(i) By the Company if, at any time prior to receipt of the Company Stockholder Approval, (i) the Company Board of Directors has received a Company Superior Proposal, (ii) in light of such Company Superior Proposal, the Company Board of Directors has determined, in good faith by resolution duly adopted after consultation with outside counsel, that it is necessary for the Company Board of Directors to withdraw, amend or modify its approval or recommendation of this Agreement or the Merger in order to comply with its fiduciary duties to the stockholders of the Company under applicable Law, (iii) the Company has provided written notice of the determination described in clause (ii) above to the Parent, which notice has attached to it a copy of the definitive agreement or

A-56

---

Table of Contents

agreements containing all of the terms and conditions of such Company Superior Proposal, (iv) at least three business days following receipt by the Parent of the notice referred to in clause (iii) above, and after taking into account any revised proposal made by the Parent following receipt of the notice referred to in clause (iii) above, such Company Superior Proposal remains a Company Superior Proposal and the Company Board of Directors has again made the determination referred to in clause (ii) above (it being understood and agreed that any change to the financial or other material terms of such Company Superior Proposal shall require a new notice to the Parent under clause (iii) above and a new three-business-day period under this clause (iv)), (v) the Company has not breached Section 4.11 in any material respect, (vi) concurrent with such termination, the Company Board of Directors approves, and the Company enters into, a definitive agreement providing for the implementation of a Company Superior Proposal and (vii) the Company, at or prior to any termination pursuant to this Section 8.1(i) pays to Parent the Termination Fee.

A-57

---

Table of Contents

A-58

---

Table of Contents

	Brooks Automation, Inc.
	15 Elizabeth Drive
	Chelsmford, MA 01824
	Attn: General Counsel
	Telephone: (978) 721-3371
	Facsimile: (978) 262-2511

	with a copy to:

	Ropes & Gray LLP
	One International Place
	Boston, Massachusetts 02110
	Attn: Winthrop G. Minot and Shari H. Wolkon
	Telephone: (617) 951-7364/ (617) 951-7861
	Facsimile: (617) 951-7050

	Helix Technology Corporation
	Nine Hampshire Street
	Mansfield, MA 02048
	Attn: Chief Financial Officer
	Telephone: (508) 337-5055
	Facsimile: (508) 337-5505

	with a copy to:

	Palmer & Dodge, LLP
	111 Huntington Avenue
	Boston, Massachusetts 02199
	Attn: Matthew J. Gardella
	Telephone: (617) 239-0789
	Facsimile: (617) 227-4420

A-59

---

Table of Contents

A-60

---

Table of Contents

A-61

---

Table of Contents

	BROOKS AUTOMATION, INC.

	By	/s/ Edward C. Grady

	Name: Edward C. Grady

	Title:	President and Chief Executive Officer

	MT. HOOD CORPORATION

	By:	/s/ Robert W. Woodbury, Jr.

	Name: Robert W. Woodbury, Jr.

	Title:	President

	HELIX TECHNOLOGY CORPORATION

	By	/s/ James Gentilcore

	Name: James Gentilcore

	Title:	President and Chief Executive Officer

A-62

---

Table of Contents

B-1

---

Table of Contents

	Very truly yours,
	/s/ NEEDHAM & COMPANY, LLC
	NEEDHAM & COMPANY, LLC

B-2

---

Table of Contents

	i)	reviewed certain publicly available financial statements and other business and financial information of the Company and Parent;
	ii)	reviewed certain internal financial statements and other financial and operating data concerning the Company and Parent prepared by the managements of the Company and Parent, respectively;
	iii)	reviewed certain financial projections prepared by the managements of the Company and Parent;
	iv)	discussed the past and current operations and financial condition and the prospects of the Company and Parent with senior executives of the Company and Parent, respectively;
	v)	reviewed the pro forma impact of the Merger on Parent’s earnings per share;
	vi)	discussed potential strategic, financial and operational benefits anticipated from the Merger with senior executives of the Company and Parent;
	vii)	reviewed the reported prices and trading activity for the Company Common Stock and the Parent Common Stock;
	viii)	compared the financial performance of the Company and Parent and prices and trading activity of the Company Common Stock and the Parent Common Stock with those of certain other comparable publicly-traded companies;
	ix)	reviewed the financial terms, to the extent publicly available, of certain comparable acquisition transactions;
	x)	participated in discussions and negotiations among representatives of the Company and Parent and their financial and legal advisors;
	xi)	reviewed the Merger Agreement and certain related documents; and
	xii)	performed such other analyses and considered such other factors as we have deemed appropriate.

C-1

---

Table of Contents

	Very truly yours,
	MORGAN STANLEY & CO. INCORPORATED

C-2