Document:

exv10w02

Exhibit 10.02

BROOKS AUTOMATION, INC.

AMENDED AND RESTATED 2000 EQUITY INCENTIVE PLAN 

(formerly known as the 2000 Combination Stock Option Plan)

Restated as of May 6, 2008

Section 1. Purpose

     The purpose of the Brooks Automation, Inc. Amended and Restated 2000 Equity Incentive Plan
(the “Plan”) is to attract and retain key employees, independent directors, consultants and
advisors. The Plan provides an incentive for these Participants to assist Brooks Automation, Inc.
(the “Company”) to achieve long-range performance goals, and to enable them to participate in the
long-term growth of the Company.

Section 2. Definitions

	(a)	 	“Affiliate” means any corporation or other entity that stands in a relationship to the
Company that would result in the Company and such corporation or other entity being treated as
one employer under Section 414(b) or Section 414(c) of the Code, except that in determining
eligibility for the grant of a Stock Option or SAR by reason of service for an Affiliate,
Sections 414(b) and 414(c) of the Code shall be applied by substituting “at least 50%” for “at
least 80%” under Section 1563(a)(1), (2) and (3) of the Code and Treas. Regs. § 1.414(c)-2;
provided, that to the extent permitted under Section 409A, “at least 20%” shall be used in
lieu of “at least 50%”; and further provided, that the lower ownership threshold described in
this definition (50% or 20% as the case may be) shall apply only if the same definition of
affiliation is used consistently with respect to all compensatory stock options or stock
awards (whether under the Plan or another plan). The Company may at any time by amendment
provide that different ownership thresholds (consistent with Section 409A of the Code) apply.
Notwithstanding the foregoing provisions of this definition, except as otherwise determined by
the Committee a corporation or other entity shall be treated as an Affiliate only if its
employees would be treated as employees of the Company for purposes of the rules promulgated
under the Securities Act of 1933, as amended, with respect to the use of Form S-8.
	 
	(b)	 	“Award” means any Option, Stock Appreciation Right, Performance or Award Share, or Restricted
Stock awarded under the Plan.
	 
	(c)	 	“Board” means the Board of Directors of the Company.
	 
	(d)	 	“Code” means the Internal Revenue Code of 1986, as amended from time to time.
	 
	(e)	 	“Committee” means the Compensation Committee of the Board, or such other Committee of not
less than two independent members of the Board appointed by the Board to administer the Plan.
If at any time the Compensation Committee consists of members, one or more of whom do not
qualify as independent, non-employee or outside directors (for purposes of applicable stock
exchange rules, the requirements of Rule 16b-3 promulgated under the Exchange Act, and the
requirements of Section 162(m) of the Code), it shall act in respect of the Plan through a
subcommittee of two or more members, all of whom so qualify, and all references herein to the
Committee shall be deemed to refer to such subcommittee.
	 
	(f)	 	“Common Stock” or “Stock” means the Common Stock, par value $.01 per share, of the Company.
	 
	(g)	 	“Company” means Brooks Automation, Inc.

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	(h)	 	“Covered Transaction” means any of (i) a consolidation, merger, or similar transaction or
series of related transactions, including a sale or other disposition of stock, in which the
Company is not the surviving corporation or which results in the acquisition of all or
substantially all of the Company’s then outstanding common stock by a single person or entity
or by a group of persons and/or entities acting in concert, (ii) a sale or transfer of all or
substantially all the Company’s assets, or (iii) a dissolution or liquidation of the Company.
Where a Covered Transaction involves a tender offer that is reasonably expected to be followed
by a merger described in clause (i) (as determined by the Committee), the Covered Transaction
shall be deemed to have occurred upon consummation of the tender offer.
	 
	(i)	 	“Designated Beneficiary” means the beneficiary designated by a Participant, in a manner
determined by the Committee, to receive amounts due or exercise rights of the Participant in
the event of the Participant’s death. In the absence of an effective designation by a
Participant, Designated Beneficiary shall mean the Participant’s estate.
	 
	(j)	 	“Exchange Act” means the Securities Exchange Act of 1934, as amended from time to time, or
any successor statue.
	 
	(k)	 	“Fair Market Value” means, (i) the closing sales price, if any, on a national securities
exchange or automated quotation system on the date as of which Fair Market Value is being
determined or, if none, shall be the closing sales price on the nearest trading date before
that date; and (ii) if the Common Stock is then traded on an exchange or system which does not
have sale price reporting, the mean between the average of the “Bid” and the average of the
“Ask” prices, if any, as reported for the date as of which Fair Market Value is being
determined. Fair Market Value shall be determined in a manner consistent with the
requirements under Section 409A of the Code.
	 
	(l)	 	“Incentive Stock Option” means an option to purchase shares of Common Stock awarded to a
Participant under Section 6 which is intended to meet the requirements of Section 422 of the
Code or any successor provision.
	 
	(m)	 	“Non-Qualified Stock Option” means an option to purchase shares of Common Stock, awarded to a
Participant under Section 6, which does not meet the requirements of Section 422 of the Code
or any successor provision. Each option granted under the Plan shall be deemed to be, by its
terms, a Non-Qualified Stock Option unless it is expressly designated as an Incentive Stock
Option.
	 
	(n)	 	“Option” means a Nonqualified Stock Option or Incentive Stock Option.
	 
	(o)	 	“Participant” means a person eligible pursuant to Section 3 hereof and selected by the
Committee to receive an Award under the Plan.
	 
	(p)	 	“Performance Cycle” or “Cycle” means the period of time selected by the Committee during
which performance is measured for the purpose of determining the extent to which a Performance
Award has been earned.
	 
	(q)	 	“Performance Award” means an Award awarded to a Participant under Section 8 that is subject
to one or more specified performance conditions, other than the mere passage of time, the
satisfaction of which is a condition for the grant, exercisability, vesting or full enjoyment
of an Award. The term “specified performance condition” means, in the case of Performance
Awards

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other than Options or SARs, an objectively determinable measure of performance relating to any
or any combination of the following (measured either absolutely or by reference to an index or
indices and determined either on a combined basis or, as the context permits, on a divisional,
subsidiary, line of business, project or geographical basis or in combinations thereof): sales;
revenues; assets; expenses; earnings before or after deduction for all or any portion of
interest, taxes, depreciation or amortization, whether or not on a continuing operations or an
aggregate or per share basis; return on equity, investment, capital or assets; one or more
operating ratios; borrowing levels, leverage ratios or credit rating; market share; capital
expenditures; cash flow; stock price; stockholder return; sales of particular products or
services; customer acquisition or retention; acquisitions and divestitures (in whole or in
part); joint ventures and strategic alliances; spin-offs, split-ups and the like;
reorganizations; or recapitalizations, restructurings, financings (issuances of debt or equity)
or refinancings. Such criteria and any targets with respect thereto determined by the Committee
need not be based on an increase, a positive or improved result or avoidance of loss. To the
extent consistent with the requirements for satisfying the performance-based compensation
exception under Section 162(m), the Committee may provide in the case of any Award intended to
qualify for such exception that one or more of the criteria applicable to such Award will be
adjusted in an objectively determinable manner to reflect events (for example, but without
limitation, acquisitions or dispositions) occurring during the performance period that affect
the applicable criteria.

	(r)	 	“Permanent Disability” has the meaning specified in Section 22(e)(3) of the Code.
	 
	(s)	 	“Restricted Period” means the period of time selected by the Committee during which a share
of Restricted Stock may be forfeited to the Company.
	 
	(t)	 	“Restricted Stock” means shares of Common Stock subject to forfeiture, awarded to a
Participant under Section 9.
	 
	(u)	 	“Stock Appreciation Right” or “SAR” means a right to receive any excess in value of shares of
Common Stock over the exercise price, awarded to a Participant under Section 7.
	 
	(v)	 	“Stock Unit” means an award of Common Stock and/or other rights granted as units that are
valued in whole or in part by reference to, or otherwise based on, the value of Common Stock,
awarded to a Participant under Section 10.

Section 3. Eligibility

     All key employees, independent directors, consultants and advisors of the Company or any
Affiliate capable of contributing significantly to the successful performance of the Company, other
than a person who has irrevocably elected not to be eligible, are eligible to be selected by the
Committee to be Participants in the Plan.

Section 4. Stock Available for Awards

	(a)	 	Subject to adjustment under subsection (b), Awards may be made under the Plan to acquire not
in excess of 9,000,000 shares of Company Common Stock. Subject to adjustment under subsection
(b), the maximum aggregate number of shares of the Company’s Common Stock for which option
grants may be made to any person during any fiscal year shall be 500,000 shares and the maximum aggregate number of shares of the Company’s Common Stock for which

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	 	 	other awards
may be made to any one person during any fiscal year shall be 250,000 shares; provided, however,
that up to an additional 100,000 shares of Common Stock may be granted as other awards during
any fiscal year to the Chief Executive Officer of the Company as an inducement to become
employed (or reemployed) by the Company. If any Award in respect of shares of Common Stock
expires or is terminated unexercised or is forfeited for any reason or settled in a manner that
results in fewer shares outstanding than were initially awarded, including without limitation
the surrender of shares in payment for the Award or any tax obligation thereon, the shares
subject to such Award or so surrendered, as the case may be, to the extent of such expiration,
termination, forfeiture or decrease, shall again be available for award under the Plan. Shares
issued under the Plan may consist in whole or in part of authorized but unissued shares or
treasury shares. No Incentive Stock Option may be issued after the following dates: (x)
January 6, 2010 with respect to the 1,000,000 shares of the Company’s Common Stock authorized
for issuance hereunder approved by the stockholders of the Company on February 24, 2000; (y)
December 13, 2011 with respect to the additional 5,000,000 shares of the Company’s Common Stock
authorized for issuance hereunder approved by the stockholders of the Company on May 13, 2002,
and (z) January 25, 2016 with respect to the additional 3,000,000 shares of the Company’s Common
Stock authorized for issuance hereunder approved by the stockholders of the Company on March 7,
2006.

	(b)	 	In the event that the Committee determines that any stock dividend, recapitalization,
reorganization, merger, consolidation, or other similar transaction affects the Common Stock
such that an adjustment is required in order to preserve the benefits or potential benefits
intended to be made available under the Plan, then the Committee shall equitably adjust any or
all of (i) the number and kind of shares in respect of which Awards may be made under the
Plan, (ii) the number and kind of shares subject to outstanding Awards, and (iii) the award,
exercise or conversion price with respect to any of the foregoing, and if considered by the
Committee to be appropriate, the Committee may make provision for a cash payment with respect
to an outstanding Award, provided that the number of shares subject to any Award shall always
be a whole number.

Section 5. Administration

	(a)	 	The Plan shall be administered by the Committee. Except where the full Board of Directors
serves as the Committee, the Committee shall serve at the pleasure of the Board, which may
from time to time appoint additional members of the Committee, remove members and appoint new
members in substitution for those previously appointed, and fill vacancies however caused. A
majority of the Committee shall constitute a quorum and the acts of a majority of the members
present at any meeting at which a quorum is present shall be deemed the action of the
Committee. To the extent permitted by applicable law, the Committee may delegate (i) to one
or more if its members such of its duties, powers and responsibilities as it may determine;
(ii) to one or more officers of the Company the power to grant rights or options to the extent
permitted by Section 157(c) of the General Corporation Law of the State of Delaware; (iii) to
one or more officers of the Company the authority to allocate other Awards among such persons
(other than officers of the Company) eligible to receive Awards under the Plan as such
delegated officer or officers determine consistent with such delegation, provided, that with
respect to any delegation described in this clause (iii), the Committee (or a properly
delegated member or members of the Committee) shall have authorized the issuance of a
specified number of shares of stock under such Awards and shall have specified the
consideration, if any, to be paid therefor; and (iv) to such employees or other persons as it
determines such ministerial tasks as it deems appropriate. In the event of any delegation
described in the preceding sentence, the term “Committee” shall include the person or persons
so delegated to the extent of such delegation.

	(b)	 	Subject to the express provisions of this Plan and provided that all actions taken shall be
consistent with the purposes of the Plan, the Committee shall have full and complete authority
and the sole discretion to: (i) determine those persons eligible under Section 3; (ii) select those 

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	 	 	persons to whom Awards shall be granted under the Plan; (iii) determine the time or times
when Awards shall be granted; (iv) establish the terms and conditions upon which Awards may be
exercised; (v) alter any restrictions or conditions upon any Awards; and (vi) adopt rules and
regulations, establish, define and/or interpret any other terms and conditions, and make all
other determinations (which may be on a case-by-case basis) deemed necessary or desirable for
the administration of the Plan.

	(c)	 	The Terms of each type of Award need not be identical, and the Committee need not treat
Participants uniformly. Except as otherwise provided by the Plan or a particular Award, any
determination with respect to an Award may be made by the Committee at the time of Award or at
any time thereafter.
	 
	(d)	 	In making its determinations hereunder, the Committee shall take into account the nature of
the services rendered or to be rendered by the Participant, their present and potential
contributions to the success of the Company, and such other factors as the Committee, in its
discretion, shall deem relevant in order to accomplish the purposes of the Plan.

Section 6. Stock Options

	(a)	 	General. Subject to the provisions of the Plan, the Committee may award Incentive
Stock Options and Non-Qualified Stock Options and determine the number of shares to be covered
by each Option, the option price therefore and the conditions and limitations applicable to
the exercise of the Option. Any Option granted under this Plan shall be upon such terms and
conditions not inconsistent with this Plan as the Committee may determine. At the time of
grant of any Option, the Committee shall specify whether the Option is intended to be an
Incentive Stock Option or a Non-Qualified Stock Option.
	 
	(b)	 	Price. The price at which any shares of Stock may be purchased pursuant to the
exercise of an Option shall be determined by the Committee but may not be less than the
greater of (i) the minimum legal consideration required under the laws of the jurisdiction in
which the Company is then organized or (ii) the Fair Market Value of the Stock on the date of
grant of the Option.
	 
	(c)	 	Re-pricing. The Committee shall not reprice an Option once it has been granted under
this Plan by reducing the exercise price of the Option or canceling an Option and regranting a
new Option for a similar number of shares at a lower price, except as expressly provided in
Section 11(f), (g) or (h).
	 
	(d)	 	Period of Option.  Each Option granted under this Plan shall continue in effect for
such period not exceeding seven years as the Committee shall determine.
	 
	(e)	 	Exercise of Options:

	 	(i)	 	Options may be exercised in whole or in part at such time and in
such manner as the Committee may determine.
	 
	 	(ii)	 	The purchase price of shares of Stock upon exercise of an Option
shall be paid by the Option holder in full upon exercise and may be paid as the
Committee may determine in its sole discretion in any combination of: (i) cash or
check acceptable to the Committee and payable to the order of the Company; (ii)
delivery of shares of Common Stock (valued at Fair Market Value at the date of

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	 	 	 	purchase of the Common Stock subject to the Option); or (iii) such other means
as the Committee may permit; provided, however, that payment of the
exercise price by delivery of shares of Common Stock of the Company owned by the
Option holder may be made only if such payment does not result in a charge to
earnings for financial accounting purposes, as determined by the Committee.
	 
	 	(iii)	 	With the consent of the Committee, payment of the exercise price may
also be made by delivery of a properly executed exercise notice to the Company,
together with a copy of irrevocable instructions to a broker to deliver promptly to
the Company the payment to pay the exercise price. To facilitate such
arrangements, the Company may enter into agreements for coordinating procedures
with one or more securities brokerage firms. The date of delivery of such exercise
notices shall be deemed the date of exercise.
	 
	 	(iv)	 	The Committee may impose such conditions with respect to the exercise
of Options, including conditions relating to applicable federal or state securities
laws, as it considers necessary or advisable, including making the Common Stock
issued upon exercise subject to restrictions on vesting or transferability, or to
risk of forfeiture, upon the happening of such events as the Committee may
determine, any of which may be accelerated or waived in the Committee’s sole
discretion.
	 
	 	(v)	 	No shares of Common Stock shall be issued upon exercise of any Option
under this Plan until full payment in the form approved by the Committee has been
made and all other legal requirements applicable to the issuance or transfer of
such shares and such other requirements as are consistent with the Plan have been
complied with to the satisfaction of the Committee.

Section 7. Stock Appreciation Rights

	(a)	 	Subject to the provisions of the Plan, the Committee may grant Awards under the Plan of Stock
Appreciation Rights to Participants.

	(b)	 	The base value from which appreciation is to be measured for a Stock Appreciation Right shall
be an amount (payable in cash or stock) determined by the Committee, but in no event shall
such amount be less than the greater of (i) the Fair Market Value of a share of Common Stock
on the date the Stock Appreciation Right is granted or (ii) the minimum amount permitted by
applicable laws, rules or policies of any regulatory authority or stock exchange. Each Stock
Appreciation Right granted shall entitle a Participant upon exercise to an amount equal to (i)
excess of (A) the Fair Market Value on the exercise date of one share of Common Stock over (B)
the base value from which appreciation is to be measured, times (ii) the number of shares of
Common Stock covered by the exercisable portion of the Stock Appreciation Right. Stock
Appreciation Rights may be exercised from time to time upon actual receipt by the Company of
written notice of exercise stating the portion of the Stock Appreciation Right that is being
exercised. No fractional shares will be issued in payment for Stock Appreciation Rights. If
there are fractional shares, then such fractional shares shall be rounded down to the next
whole share.

	(c)	 	The Company may impose, in its sole discretion, such conditions upon the exercisability or
transferability of Stock Appreciation Rights as it may deem fit. A Stock Appreciation Right

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	 	 	shall expire on a date designated by the Committee that is not later than seven years after
the date of grant of the Stock Appreciation Right.

Section 8. Performance Awards

	(a)	 	Subject to the provisions of the Plan, the Committee may grant Awards of Performance Awards
and determine the number of such shares for each Performance Cycle and the duration of each
Performance Cycle. There may be more than one Performance Cycle in existence at any one time,
and the duration of Performance Cycles may differ from each other. The payment value of
Performance Awards shall be equal to the product of (A) the number of shares granted times (B)
the Fair Market Value of the Common Stock on the date the Performance Awards are earned or, in
the discretion of the Committee, on the date the Committee determines that the Performance
Awards have been earned.

	(b)	 	The Committee shall establish performance goals for each Performance Cycle for the purpose of
determining the extent to which Performance Awards awarded for such Performance Cycle are
earned, on the basis of such criteria and to accomplish such objectives as the Committee may
from time to time select. During any Performance Cycle, the Committee may adjust the
performance goals for such Performance Cycle as it deems equitable in recognition of unusual
or non-recurring events affecting the Company, changes in applicable tax laws or accounting
principles, or such other factors as the Committee may determine.

	(c)	 	As soon as practicable after the end of a Performance Cycle, the Committee shall determine
the number of Performance Awards which have been earned on the basis of the Participant’s
satisfaction of established performance goals. The payment values of earned Performance
Awards shall be distributed to the Participant or, if the Participant has died, to the
Participant’s Designated Beneficiary, as soon as practicable after the Committee’s
determination. The Committee shall determine, at or after the time the Award is granted,
whether payment values will be settled in whole or in part in cash or other property,
including Common Stock.

Section 9. Restricted Stock

	(a)	 	Subject to the provisions of the Plan, the Committee may grant an Award of Restricted Stock
and determine the duration of the Restricted Period during which, and the conditions under
which, the shares of Restricted Stock may be forfeited to the Company and the other terms and
conditions of such Awards. Shares of Restricted Stock may be issued for no cash consideration
or such minimum consideration as may be required by applicable law.

	(b)	 	Shares of Restricted Stock may not be sold, assigned, transferred, pledged or otherwise
encumbered, except as permitted by the Committee, during the Restricted Period. Shares of
Restricted Stock shall be evidenced in such manner as the Committee may determine. Any
certificates issued in respect of shares of Restricted Stock shall be registered in the name
of the Participant and unless otherwise determined by the Committee, deposited by the
Participant, together with a stock power endorsed in blank, with the Company. At the
expiration of the Restricted Period, the Company shall deliver such certificates to the
Participant or if the Participant has died, to the Participant’s Designated Beneficiary.

Section 10. Stock Units

	(a)	 	Subject to the provisions of the Plan, the Committee may grant Awards of Stock Units subject
to such terms, restrictions, conditions, performance criteria, vesting requirements and
payment rules as the Committee shall determine.

	(b)	 	Shares of Common Stock awarded in connection with an Award of Stock Units shall be issued for
no cash consideration or such minimum consideration as may be required by applicable law.

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Section 11. General Provisions Applicable to Awards

	(a)	 	Documentation. Each Award under the Plan shall be evidenced by a written document
delivered to the Participant specifying the terms and conditions thereof and containing such
other terms and conditions not inconsistent with the provisions of the Plan as the Committee
considers necessary or advisable to achieve the purposes of the Plan or comply with applicable
tax and regulatory laws and accounting principles. The date of Award hereunder shall be the
date upon which such Award is voted by the Committee, unless such vote provides otherwise.

	(b)	 	Committee Discretion. Each type of Award may be made alone, in addition to or in
relation to any other type of Award. Except as otherwise provided by the Plan or a particular
Award, any determination with respect to an Award may be made by the Committee at the time of
award or at any time thereafter.

	(c)	 	Settlement. The Committee shall determine whether Awards are settled in whole or in
part in cash, Common Stock, other securities of the Company, Awards or other property.

	(d)	 	Additional Provisions For Awards: The following additional conditions shall apply to
all Awards, as applicable:

	 	(i)	 	Incentive Stock Options shall be granted only to employees of the Company or of a
“parent corporation” or “subsidiary corporation” (as those terms are defined in Section 424 of
the Code) with respect to the Company;
	 
	 	(ii)	 	Each Award shall, by its terms, be transferable by the Participant
only by will or the laws of descent and distribution, and shall be exercisable
only by such Participant during his lifetime; and
	 
	 	(iii)	 	The terms and conditions of Incentive Stock Options shall be
subject to and comply with Section 422 of the Code, or any successor provision,
and any regulations thereunder.

	(e)	 	Termination of Employment. Except as provided herein, the Committee shall determine
the effect on an Award of the disability, death, retirement or other termination of employment
of a Participant and the extent to which, and the period during which, the Participant’s legal
representative, guardian or Designated Beneficiary may receive payment of an Award or exercise
rights thereunder.

	(f)	 	Consolidation or Mergers. With respect to Awards granted prior to March 7, 2006, if
the Company is to be consolidated with or acquired by another entity in a merger, sale of all
or substantially all of the Company’s assets or otherwise (an “Acquisition”), the Committee or
the board of directors of any entity assuming the obligations of the Company hereunder shall,
as to outstanding Awards, make appropriate provision for the continuation of such Awards by
substituting on an equitable basis for the shares then subject to such Awards the
consideration payable with respect to the outstanding shares of Common Stock in connection
with the Acquisition and by adjusting on an equitable basis the exercise price of such Awards
to reflect such Acquisition.

	(g)	 	Recapitalization or Reorganization. With respect to Awards granted prior to March 7,
2006, in the event of a recapitalization or reorganization of the Company (other than an
Acquisition) pursuant to which securities of the Company or of another corporation are issued
with respect to the outstanding shares of Common Stock, a Participant upon exercising rights
under an Award

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	 	 	shall be entitled to receive what he would have received if he had exercised prior to such
recapitalization or reorganization.

	(h)	 	Mergers, etc. With respect to Awards granted on or after March 7, 2006, except as
otherwise provided in an Award, the following provisions shall apply in the event of a Covered
Transaction:

	 		 	(i) Assumption or Substitution. If the Covered Transaction is one in
which there is an acquiring or surviving entity, the Committee may provide for
the assumption of some or all outstanding Awards or for the grant of new awards
in substitution therefor by the acquiror or survivor or an affiliate of the
acquiror or survivor.
	 
	 		 	(ii) Cash-Out of Awards. If the Covered Transaction is one in which
holders of Stock will receive upon consummation a payment (whether cash, non-cash
or a combination of the foregoing), the Committee may provide for payment (a
“cash-out”), with respect to some or all Awards (or portion of Awards), equal in
the case of each affected Award to the excess, if any, of (A) the fair market
value of one share of Stock (as determined by the Committee in its reasonable
discretion) times the number of shares of Stock subject to the Award or portion
of the Award, over (B) the aggregate exercise or purchase price, if any, under
the Award or portion of the Award (in the case of a Stock Appreciation Right, the
aggregate base price above which appreciation is measured), in each case on such
payment terms (which need not be the same as the terms of payment to holders of
Stock) and other terms, and subject to such conditions, as the Committee
determines.
	 
	 		 	(iii) Other Actions. If the Covered Transaction (whether or not there is
an acquiring or surviving entity) is one in which there is no assumption,
substitution or cash-out, each Award requiring exercise will cease to be
exercisable after such payment or other consideration, if any, as the Committee
deems equitable in the circumstances, as of the effective time of the Covered
Transaction.
	 
	 		 	(iv) Termination of Awards Upon Consummation of Covered Transaction.
Each Award (unless assumed pursuant to Section 11(h)(i) above), other than
outstanding shares of Restricted Stock (which shall be treated in the same manner
as other shares of Stock, subject to Section 11(h)(v) below), will terminate upon
consummation of the Covered Transaction.
	 
	 		 	(v) Additional Limitations. Any share of Stock delivered pursuant to
Section 11(h)(ii) or Section 11(h)(iii) above with respect to an Award may, in
the discretion of the Committee, contain such restrictions, if any, as the
Committee deems appropriate to reflect any performance or other vesting
conditions to which the Award was subject. In the case of Restricted Stock, the
Committee may require that any amounts delivered, exchanged or otherwise paid in
respect of such Stock in connection with the Covered Transaction be placed in
escrow or otherwise made subject to such restrictions as the Committee deems
appropriate to carry out the intent of the Plan.

	(i)	 	Modification of Incentive Stock Options. Notwithstanding the foregoing, any
adjustments made pursuant to subparagraphs (f) or (g) with respect to Incentive Stock Options
shall be made only after the Committee, after consulting with counsel for the Company,
determines whether such adjustments would constitute a “modification” of such Incentive Stock
Options (as that term is defined in Section 424 of the Code) or would cause any adverse tax
consequences for the holders of such Incentive Stock Options. If the Committee determines that such adjustments 

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	 	 	made
with respect to Incentive Stock Options would constitute a modification of such Incentive Stock
Options, it may refrain from making such adjustments.

	(j)	 	Withholding. The Participant shall pay to the Company, or make provision
satisfactory to the Committee for payment of, any taxes required by law to be withheld in
respect of Awards under the Plan no later than the date of the event creating the tax
liability. In the Committee’s discretion, such tax obligations may be paid in whole or in
part in shares of Common Stock, including shares retained from the Award creating the tax
obligation, valued at their Fair Market Value on the date of delivery. The Company and its
Affiliates may, to the extent permitted by law, deduct any such tax obligations from any
payment of any kind otherwise due to the Participant.

	(k)	 	Amendment of Award. The Committee may amend, modify or terminate any outstanding
Award, including substituting therefor another Award of the same or a different type, changing
the date of exercise or realization, provided that the Participant’s consent to such action
shall be required unless the Committee determines that the action, taking into account any
related action, would not materially and adversely affect the Participant.

Section 12. Miscellaneous

	(a)	 	No Right To Employment. No person shall have any claim or right to be granted an
Award, and the grant of an Award shall not be construed as giving a Participant the right to
continued employment. The Company expressly reserves the right at any time to dismiss a
Participant free from any liability or claim under the Plan, except as expressly provided in
the applicable Award.

	(b)	 	No Rights As Shareholder. Subject to the provisions of the applicable Award, no
Participant or Designated Beneficiary shall have any rights as a shareholder with respect to
any shares of Common Stock to be distributed under the Plan until he or she becomes the holder
thereof. A Participant to whom Common Stock is awarded shall be considered the holder of the
Stock at the time of the Award except as otherwise provided in the applicable Award.

	(c)	 	Term of Plan. This Plan shall terminate on January 25, 2016, and no Award shall be
granted under this Plan thereafter, but such termination shall not affect the validity of
Awards granted prior to the date of termination.

	(d)	 	Amendment of Plan. The Board or Committee, if so authorized by the Board, may amend,
suspend or terminate the Plan or any portion thereof at any time.

	(e)	 	Foreign Participants. Subject to the limitations set forth in Section 4 herein, the
Committee may grant Awards to Participants who reside or are employed outside the United
States on such terms and conditions as determined in the sole discretion of the Committee are
necessary or advisable to achieve the purposes of the Plan or to comply with foreign laws,
including the establishment of subplans under this Plan. Any subplans or other modifications
to Plan terms, conditions or procedures established under this Section, shall be attached as
Appendices.

	(f)	 	Governing Law. The provisions of the Plan shall be governed by and interpreted in
accordance with the laws of the State of Delaware.

	(g)	 	Indemnity. Neither the Board nor the Committee, nor any members of either, nor any
employees of the Company or any parent, subsidiary, or other affiliate, shall be liable for
any act, omission, interpretation, construction or determination made in good faith in
connection with their responsibilities with respect to this Plan, and the Company hereby
agrees to indemnify the members of the Board, the members of the Committee, and the employees
of the Company and its parent or subsidiaries in respect of any claim, loss, damage, or
expense 

-10-

 

	 	 	(including reasonable counsel fees) arising from any such act, omission, interpretation, construction or determination
to the full extent permitted by law.

	(h)	 	Section 409A. The Committee shall administer the Plan with a view toward ensuring
that Awards under the Plan that are subject to Section 409A of the Code comply with the
requirements thereof and that Options and SARs under the Plan be exempt from the requirements
of Section 409A of the Code, but neither the Committee nor any member of the Board, nor the
Company, nor any other person acting hereunder on behalf of the Company, the Committee or the
Board shall be liable to a Participant or any Designated Beneficiary by reason of the
acceleration of any income, or the imposition of any additional tax, with respect to an Award,
whether by reason of a failure to satisfy the requirements of Section 409A of the Code or
otherwise.

Dates of Approval by Board of Directors or Compensation Committee: January 6, 2000, January 23,
2001, and December 13, 2001, May 20, 2002, September 13, 2002, February 26, 2003, February 25,
2004, January 25, 2006 and May 6, 2008.

Dates of Approval by Stockholders: February 24, 2000, February 28, 2001, May 13, 2002, April 27,
2004 and March 7, 2006.

-11-exv10w03

Exhibit 10.03

BROOKS AUTOMATION, INC.

RESTRICTED STOCK AGREEMENT

     AGREEMENT made effective as of April 25, 2008, between Brooks Automation, Inc., a Delaware
corporation (the “Company”), and Robert J. Lepofsky (the “Employee”).

WITNESSETH:

     WHEREAS, as an inducement for the Employee to assist the Company to achieve long-range
performance goals and to enable the Employee to participate in the long-term growth of the Company,
the Company desires to grant to the Employee 50,000 Shares (the “Shares”) of the Company’s common
stock, (the “Common Stock”), as an inducement to the Employee to accept the position of Chief
Executive Officer of the Company; and

     WHEREAS, the grant of the Shares herein is issued as a so-called “inducement grant” to the
Employee and is not made pursuant to the Company’s Amended and Restated 2000 Equity Incentive Plan
(the “Plan”); and

     WHEREAS, it is nonetheless the intention of the parties to incorporate by reference in this
agreement the terms and conditions of the Plan and to be bound thereby in all respects except the
provisions of Section 4(a) of the Plan limiting the number of shares that can be issued to any
person in a single fiscal year.

     NOW, THEREFORE, for good and valuable consideration, receipt and sufficiency of which are
hereby acknowledged, the parties hereto agree as follows:

ARTICLE 1 — ACQUISITION OF SHARES

     1.1 Award of Shares. The Company has granted the Shares to the Employee, and the
Employee hereby accepts the Shares, subject to the terms and conditions of the Plan (other than
Section 4(a) thereof) and this Agreement. In the event of an inconsistency between this Agreement
and the Plan (other than Section 4(a) thereof), the Plan will control. All capitalized terms not
defined in this Agreement have the meaning specified in the Plan.

     1.2 Record ownership; custody of certificates, etc.

          (a) In accordance with the Plan and Section 158 of the Delaware General Corporation Law, the
Shares shall be evidenced in the books of the Company as owned by the Employee. The Shares shall be
held in uncertificated form except as the Company otherwise determines. If at any time the Shares
are represented by certificates or other evidence of ownership, the Company may retain custody of
such certificates or other evidence of ownership until such time as the Shares are either forfeited
to the Company or cease to be subject to the risk of forfeiture and transfer restrictions described
herein and in the Plan. Notwithstanding the foregoing, except as set forth herein or in the Plan
the Employee shall have the rights of an owner of the Shares, including the right to vote the
Shares and the right to dividends or other distributions.

 

 

          (b) Upon the lapsing of the restrictions described herein with respect to the Shares, the
Company shall take such steps as it determines to be necessary or appropriate to transfer
certificates or other evidence of ownership to the Employee, including, if so determined by the
Company, to a brokerage account held by or for the benefit of the Employee.

     1.3 Employee Representations. The Employee represents, warrants and covenants as
follows:

          (a) The Employee has received and reviewed the Plan and the Prospectus related to the Plan,
including the documents incorporated therein by reference.

          (b) The Employee understands that (i) the Federal income tax consequences to the Employee of
the transfer of the Shares to the Employee will vary depending upon whether the Employee makes an
election under Section 83(b) of the Internal Revenue Code of 1986, as amended (the “Code”), (ii)
the Company is not providing the Employee with any advice as to whether to make such election,
(iii) the Employee has been advised to seek the counsel of his or her own tax advisor as to
whether, and if so where and how to make such election, (iv) such election, if made, must be filed
with the Internal Revenue Service within 30 days of the date of this Agreement, and (v) the
Employee must notify the Company upon making such election.

          (c) The Employee understands, agrees and acknowledges that the Shares are subject to
restrictions on transfer and may be forfeited if the conditions of this Agreement are not
satisfied. The Employee also understands, agrees and acknowledges that if the Shares are ever
certificated the Company may, at its election and in its sole discretion, require that the
certificates have affixed thereto a legend in substantially the following form:

     “The shares of stock represented by this certificate are subject to
restrictions on transfer and a risk of forfeiture set forth in a certain
Restricted Stock Agreement between the corporation and the registered owner
of this certificate (or his or her predecessor in interest). Such Agreement
is available for inspection without charge at the principal executive offices
of the corporation.”

ARTICLE 2 — VESTING AND FORFEITURE

     2.1 Vesting and Forfeiture. For purposes of this Agreement, employment with the
Company shall include employment with a consolidated subsidiary of the Company. The Shares shall
vest as follows unless earlier forfeited in accordance with this Section 2.1:

          (a) Unless earlier vested or forfeited, the Shares will vest, if at all, based upon the
satisfaction of three performance criteria: (i) total shareholder return — i.e. fiscal year over
fiscal year change in average trailing fifteen trading day share price plus accumulated dividends,
(ii) pre-tax operating income from continuing operations (excluding special income/charges such as
patent settlements), and (iii) pre-tax return on shareholder equity — i.e. pre-tax income divided
by stockholder equity expressed as a percentage (collectively, the “Performance Factors”) and a
continuing employment requirement. Vesting of the Shares will be measured as of September

2

 

30, 2008, and again as of September 30, 2009, (each, a “Measurement Date”). The aggregate net
percentage increase in each of the three Performance Factors for the Company’s fiscal year that
includes the Measurement Date (taking into account for this purpose any percentage decrease that
may occur in any of the Performance Factors) shall be multiplied by the total number of Shares that
are not vested, determined immediately prior to the relevant Measurement Date, to determine the
number of Shares that vest as of the Measurement Date. The Employee must also be employed by the
Company on the Measurement Date to vest in any earned portion of the Shares. For example, if for
the Company’s fiscal year ending September 30, 2008, the Company’s pretax operating income
increased by 9%, its return on shareholder equity increased by 10%, and total shareholder return
increased by 51%, the Employee would vest in 70% of the Shares (i.e., in 35,000 shares).
Notwithstanding the foregoing, the Human Resources and Compensation Committee may exercise its
discretion to vest all or a part of any otherwise unvested portion of the Shares at any time if
such acceleration is in the best interests of the Company. Any Shares remaining unvested as of
October 1, 2009, shall be immediately and automatically forfeited to the Company.

          (b) If there is a Qualifying Termination of the Employee’s employment with the Company
and its subsidiaries that occurs within the one-year period following a Change in Control, any
Shares that were unvested but outstanding immediately prior to the Qualifying Termination shall be
treated as having vested immediately prior to the Qualifying Termination.

For purposes of this Section 2.1:

     (A) “Change in Control” means the occurrence of any of the events described in
subsections (i), (ii), (iii), or (iv) below:

     (i) Any Person acquires beneficial ownership (within the meaning of Rule 13d-3
promulgated under the Exchange Act) of thirty-five (35%) percent or more of either
(x) the then outstanding shares of common stock of the Company (the “Outstanding
Company Common Stock”) or (y) the combined voting power of the then outstanding
voting securities of the Company entitled to vote generally in the election of
directors (the “Outstanding Company Voting Securities”); provided, that for purposes
of this subsection (A)(i) the following acquisitions shall not constitute a Change
in Control: (I) any acquisition directly from the Company, (II) any acquisition by
the Company, (III) any acquisition by an employee benefit plan (or related trust)
sponsored or maintained by the Employer, or (IV) any Business Combination (but
except as provided in subsection (A)(iii) below a Business Combination may
nevertheless constitute a Change in Control under subsection (A)(iii)); and provided
further, that an acquisition by a Person of thirty-five percent (35%) percent or
more but less than fifty (50%) percent of the Outstanding Company Common Stock or of
the combined voting power of the Outstanding Company Voting Securities shall not
constitute a Change in Control under this subsection (A)(i) if within fifteen (15)
days of the Board’s being advised that such ownership level has been reached, a
majority of the “Incumbent Directors” (as hereinafter defined) then in office adopt
a resolution approving the acquisition of that level of securities ownership by such
Person; or

3

 

     (ii) Individuals who, as of the date hereof, constituted the Board (the
“Incumbent Directors”) cease for any reason to constitute at least a majority of the
Board; provided, that any individual who becomes a member of the Board subsequent to
the date hereof, and whose election or nomination for election was approved by a
vote of at least two-thirds of the Incumbent Directors shall be treated as an
Incumbent Director unless he or she assumed office as a result of an actual or
threatened election contest with respect to the election or removal of directors; or

     (iii) There is consummated a reorganization, merger or consolidation involving
the Company, or a sale or other disposition of all or substantially all of the
assets of the Company (a “Business Combination”), in each case unless, following
such Business Combination, (x) the Persons who were the beneficial
owners, respectively, of the Outstanding Company Common Stock and of the combined voting
power of the Outstanding Company Voting Securities immediately prior to the Business
Combination beneficially own, directly or indirectly, more than 50% of, respectively, the
then outstanding shares of common stock and the combined voting power of the then
outstanding voting securities entitled to vote generally in the election of directors, as
the case may be, of the entity resulting from such Business Combination in substantially
the same proportions as their ownership immediately prior to such Business Combination of
the Outstanding Company Common Stock and of the combined voting power of the Outstanding
Company Voting Securities, as the case may be, (y) unless in connection with such Business
Combination a majority of the Incumbent Directors then in office determine that this clause
(A)(iii)(y) does not apply to such Business Combination, no Person (excluding any entity
resulting from such Business Combination or any employee benefit plan (or related trust) of
the Employer or of such corporation resulting from such Business Combination) beneficially
owns, directly or indirectly, thirty-five (35%) percent or more of, respectively, the then
outstanding shares of common stock of the corporation resulting from such Business
Combination or the combined voting power of the then outstanding voting securities of such
corporation entitled to vote generally in the election of directors, except to the extent
that such ownership existed prior to the Business Combination and (z) at least a majority
of the members of the Board resulting from such Business Combination were Incumbent
Directors at the time of the execution of the initial agreement, or of the action of the
Board, providing for such Business Combination; or

     (iv) The stockholders of the Company approve a complete liquidation or dissolution of
the Company;

provided, that if any payment or benefit payable hereunder upon or following a Change in Control
(as defined herein) would be required to comply with the limitations of Section 409A(a)(2)(A)(v) of
the Code and the guidance thereunder in order to avoid an additional tax under Section 409A of the
Code, such payment or benefit shall be made only if such Change in Control constitutes a change in
ownership or control of the Company, or a

4

 

change in ownership of the Company’s assets, described in
IRS Notice 2005-1, the final regulations under Section 409A of the Code, or any successor guidance.

     (B) “Qualifying Termination” means a termination by the Company or by a subsidiary of
the Company of the Employee’s employment with the Company and its subsidiaries, other than a
termination for Cause.

     (C) “Cause” means (i) the Employee’s willful failure to perform, or serious negligence in the
performance of, the Employee’s duties and responsibilities for the Company or any of its
subsidiaries that remains uncured, or continues, beyond the fifteenth (15th) day
following the date on which the Company gives the Employee notice specifying in reasonable detail
the nature of the failure or negligence; (ii) fraud, embezzlement or other dishonesty with respect
to the Company or any of its subsidiaries
or customers; (iii) conviction of, or a plea of guilty or nolo contendere with respect to,
a felony or to any crime (whether or not a felony) that involves moral turpitude; or (iv)
breach of fiduciary duty or violation of any covenant of confidentiality, assignment of
rights to intellectual property, non-competition or non-solicitation of customers or
employees; provided, that if at the time of termination of employment the Employee is party
to an employment agreement or similar agreement with the Company or any of its subsidiaries
that includes a definition of “Cause”, the definition contained in such employment
agreement or similar agreement shall apply for purposes of this Section 2.1 in lieu of the
definition set forth above in this clause (C).

     (D) “Board” means the Board of Directors of the Company.

     (E) “Employer” means the Company and its subsidiaries.

     (F) “Person” means any individual, entity or other person, including a group within
the meaning of Sections 13(d) or 14(d)(2) of the Exchange Act.

     (G) “Exchange Act” means the Securities Exchange Act of 1934, as amended.

     2.2 Restrictions on Transfer.

          (a) Except as otherwise provided in subsection (b) below, for so long as any of the Shares are
subject to a risk of forfeiture as described above, the Employee shall not sell, assign, transfer,
pledge, hypothecate or otherwise dispose of, by operation of law or otherwise (collectively
“transfer”), any such Shares or any interest therein. Any attempted transfer in contravention of
the foregoing shall be null and void. The Company shall not be required to transfer record
ownership on its books of any Shares subject to the restrictions herein that have been sold,
assigned or otherwise transferred, hypothecated or disposed of in violation of this Agreement.

5

 

          (b) Once the risk of forfeiture and the transfer restrictions described above lapse as to any
Shares, such Shares may be sold, transferred or otherwise disposed of subject only to the
restrictions of applicable law, including applicable securities law, and to any insider-trading or
similar restrictions that may be imposed by the Company.

ARTICLE 3 — MISCELLANEOUS

     3.1 Adjustments for Stock Splits, Stock Dividends, etc. If there is any stock split,
reverse stock split, stock dividend, stock distribution or other reclassification of the Common
Stock, any and all new, substituted or additional securities to which the Employee is entitled by
reason of his ownership of the Shares shall be immediately subject to the risk of forfeiture and
transfer restrictions described herein in the same manner and to the same extent, if any, as such
Shares.

     3.2 Restrictions on Distributions. If at any time while the Shares are subject to the
risk of forfeiture and transfer restrictions described herein there is a dividend (other than a
stock
dividend described in Section 3.1) or other distribution with respect to the Shares, whether of
cash, Common Stock, other securities or other property, the Company may require that the cash,
securities, or other property so dividended or distributed be subjected to restrictions (including,
without limitation, if the Company so determines, by holding any such amounts in escrow) similar to
those to which the Shares are then subject.

     3.3 Withholding Taxes.

          (a) Pursuant to applicable federal, state, local or foreign laws, the Company may be required
to collect income or other taxes on the transfer of the Shares to the Employee, the lapse of a
restriction placed on the Shares, or at other times. The Company may require, at such time as it
considers appropriate, that the Employee pay the Company the amount of any taxes that the Company
may determine is required to be withheld or collected, and the Employee shall comply with the
requirement or demand of the Company. The Company may withhold, collect or offset against any
amount owed by the Company to the Employee, the amount of any such taxes in any manner (including,
without limitation, by payment in whole or in part in shares of Common Stock, including the Shares,
valued at the Fair Market Value, by check, or by offsetting such amount against compensation
otherwise due to the Employee), if in its sole discretion it deems any such method to be an
appropriate method for withholding or collecting taxes.

      
    (b) If the Employee elects, in accordance with Section 83(b) of the Code, to recognize
ordinary income in the year of acquisition of the Shares, the Company may require that the
Employee, at the time of such election, make an additional payment for withholding tax purposes
based on the difference, if any, between the purchase price for such Shares and the fair market
value of such Shares.

     3.4 No Rights To Employment. Nothing contained in this Agreement shall be
construed as giving the Employee any right to be retained as an employee of the Company.

6

 

     3.5 Waiver; Disposition of Stock. From time to time the Company may waive its rights
hereunder either generally or with respect to one or more specific transfers which have been
proposed, attempted or made. Each such waiver shall be effective only in the specific instance and
for the purpose for which it was given, and shall not constitute a continuing waiver.

     3.6 Successors and Assigns; Assignment. This Agreement shall be binding upon the
parties hereto and their heirs, representatives, successors and assigns. The Company may assign its
rights hereunder either generally or from time to time.

     3.7 Notices. All notices to a party hereto shall be in writing and shall be deemed to
have been adequately given if delivered in person or mailed, postage pre-paid and registered or
certified mail or federal express or other recognized commercial courier service:

If to the Company:

Brooks Automation, Inc.

15 Elizabeth Drive

Chelmsford, Massachusetts 01824

Attention: Chief Financial Officer

If to Employee:

Robert J. Lepofsky

PO Box 81367

Wellesley Hills, Massachusetts 02481

or to such other address as any party may from time to time designate for itself by notice in
writing given to the other parties hereto.

     3.8 Amendments. This Agreement may be amended or modified in whole or in part only by
an instrument in writing signed by the Company and the Employee.

     3.9 Entire Agreement. This Agreement constitutes the entire agreement between the
parties, and all premises, representations, understandings, warranties and agreements with
reference to the subject matter hereof have been expressed herein or in the documents incorporated
herein by reference.

     3.10 Applicable Law; Severability. This Agreement shall be governed by and construed
and enforced in accordance with Delaware law. Wherever possible, each provision of this Agreement
shall be interpreted in such manner as to be effective and valid under applicable law, but if any
provision hereof shall be prohibited by or invalid under any such law, that provision shall be
ineffective only to the extent of such prohibition or invalidity, without invalidating or
nullifying the remainder of that provision or any other provisions of this Agreement.

7

 

     3.11 Counterparts. This Agreement may be executed in multiple counterparts, each of
which shall be deemed in original but all of which together shall constitute one and the same
instrument.

     3.12 Effect of Headings. Any table of contents, title of an article or section heading
herein contained is for convenience or reference only and shall not affect the meaning of
construction of any of the provisions hereof.

     IN WITNESS WHEREOF, the Employee has hereunto set his or her hand and the Company has
authorized this instrument to be signed by its officers thereunder duly authorized, effective as an
instrument under seal.

	 	 	 	 	 
	BROOKS AUTOMATION, INC.

 	 	 
	By:  	/s/ Thomas S. Grilk
 	 	 
	 	Name:  	Thomas S. Grilk 	 	 
	 	Title:  	Sr. Vice President, General Counsel & Secretary 	 	 

	 	 	 	 	 
	EMPLOYEE

 	 	 
	/s/
Robert J. Lepofsky
 	 	 
	Name:  	Robert J. Lepofsky 	 	 

8

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