Exhibit 10.28

CRAY INC.

AMENDED AND RESTATED 2001 EMPLOYEE STOCK PURCHASE PLAN

(as amended and restated March 1, 2011)

1. Purposes.

The Cray Inc. Amended and Restated 2001 Employee Stock Purchase Plan (the
“Plan”) is intended to provide additional incentives to employees and a
convenient means by which eligible employees of the Company may purchase the
Company’s shares of Common Stock and a method by which the Company may assist
and encourage such employees to become shareholders of the Company.

2. Definitions.

As used herein, the following definitions apply:

(a) “Base Salary” means the gross amount of the participant’s base salary for
each payroll period, including incentive bonuses, overtime, commissions and any
pre-tax contributions made by the Participant to any Code Section 401(k) salary
deferral plan or any Code Section 125 cafeteria benefit program, but excluding
any severance pay, hiring or relocation bonuses and pay in lieu of vacation and
sick leave.

(b) “Board” means the Company’s Board of Directors.

(c) “Code” means the Internal Revenue Code of 1986, as amended from time to
time.

(d) “Common Stock” means the Company’s common stock.

(e) “Company” means Cray Inc. a Washington corporation, and all subsidiaries of
Cray Inc. designated by the Plan Administrator as participating in the Plan and
any corporate successor to all or substantially all of the assets or voting
stock of Cray Inc. which shall by appropriate action adopt the Plan.

(f) “Eligible Employee” means any employee of the Company, other than an
employee whose customary employee is for 20 hours or less per week or whose
customary employment is for not more than 5 months per calendar year. No
employee who would after an

 

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offering pursuant to the Plan own or be deemed (under Section 425(d) of the
Code) to own stock (including any stock that may be purchased under any
outstanding options) possessing 5% or more of the total combined voting power or
value of all classes of stock of the Company shall be eligible to participate in
the Plan.

(g) “Enrollment Date” means the first day of each Offering Period.

(h) “Offering Period” shall mean the three-month or other period selected by the
Plan Administrator during which Participants may purchase shares of the Common
Stock. Unless otherwise determined by the Plan Administrator, Offering Periods
generally shall run from March 16 through June 15, June 16 through
September 15, September 16 through December 15, and December 16 through
March 15.

(i) “Participant” means any Eligible Employee of the Company who is actively
participating in the Plan.

(j) “Plan Administrator” shall mean the Compensation Committee of the Board, as
appointed from time to time by the Board.

3. Administration.

(a) Powers. The Plan Administrator shall have full authority to administer this
Plan, including, without limitation, authority to interpret and construe any
provision of this Plan; to determine the Offering Periods and the maximum number
of shares of Common Stock which may be purchased in any one Offering Period; to
determine, in accordance with Section 7(c), the fair market value of the Common
Stock on any date; to prescribe, amend and rescind rules and regulations
relating to this Plan; within law, to waive or modify any term or provision
contained in this Plan or in any right to purchase shares of Common Stock under
this Plan; to authorize any person to execute on behalf of the Company any
instrument required to effectuate this Plan; and to make all other
determinations deemed necessary or advisable for the administration for this
Plan. The interpretation and construction by the Plan Administrator of any terms
or provisions of this Plan, any right issued hereunder or of any rule or
regulation promulgated in connection herewith and all actions taken by the Plan
Administrator shall be conclusive and binding on all interested parties. The
Plan Administrator may delegate administrative functions to individuals who are
officers or employees of the Company.

(b) Limited Liability. No member of the Board of Directors or the Plan
Administrator or officer of the Company shall be liable for any action or
inaction of the entity or body, or another person or, except in circumstances
involving bad faith, of himself or herself. Subject

 

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only to compliance with explicit provisions hereof, the Board and Plan
Administrator may act in their absolute discretion in all matters related to
this Plan.

4. Offering Periods.

(a) Determination. Shares of Common Stock shall be offered for purchase under
this Plan through a series of successive Offering Periods, each to be of a
duration of three months, all as selected by the Plan Administrator, until such
time as the maximum number of shares of Common Stock available for issuance
under the Plan shall have been purchased or the Plan shall have been sooner
terminated in accordance with Sections 10 and 11(b).

(b) Separate Purchase Rights. The Participant shall be granted a separate
purchase right for each Offering Period in which he/she participates. The
purchase right shall be granted on the Enrollment Date on which such individual
first joins the Offering Period in effect under the Plan and shall be
automatically exercised for successive Offering Periods, unless the Participant
withdraws from the Plan.

5. Eligibility and Participation.

(a) Enrollment Dates. An individual who is an Eligible Employee on the start
date of the Offering Period may enter that Offering Period on such start date,
provided he/she enrolls in the Offering Period before such date in accordance
with Section 5(b) below. That start date shall then become such individual’s
Enrollment Date for the Offering Period, and on that date such individual shall
be granted his/her purchase right for the Offering Period. Should such Eligible
Employee not enter the Offering Period on the start date, then he/she may not
subsequently join that particular Offering Period on any later date.

(b) Enrollment Forms. To participate for a particular Offering Period, the
Eligible Employee must complete the enrollment forms prescribed by the Plan
Administrator (including the payroll deduction authorization) and file such
forms with the Plan Administrator at least 10 business days before his/her
scheduled Enrollment Date unless the Participant has participated in the
previous Offering Period and has not submitted a withdrawal form to the Company.

(c) Payroll Deductions. The payroll deduction authorized by the Participant for
purposes of acquiring shares of Common Stock under the Plan shall be at a rate
of not less than $25.00 per semi-monthly pay period nor more than 15% of the
Base Salary paid to the Participant during each Offering Period, unless the Plan
Administrator consents to a lower amount or higher rate for all Participants.
The deduction rate so authorized shall continue in effect for the remainder of
the Offering Period.

 

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A Participant may change the amount of his or her payroll deduction for a
subsequent Offering Period by filing an amended payroll deduction form at least
10 business days prior to the commencement of such subsequent Offering Period.

Payroll deductions will automatically cease upon the termination of the
Participant’s purchase right in accordance with the applicable provisions of
Section 7 below.

(d) Rule 16b-3. Employees who are officers of the Company may participate only
in accordance with Rule 16b-3 under the Securities Exchange Act of 1934, as in
effect from time to time.

(e) Participation Voluntary. Participation in this Plan shall be voluntary.

6. Stock Subject to Plan.

(a) Total Number. The total number of shares of Common Stock which may be issued
under this Plan shall not exceed 1,750,0001 shares (subject to adjustment under
Section 6(b) below).

(b) Changes to Capitalization. In the event any change is made to the Company’s
outstanding Common Stock by reason of any stock dividend, stock split,
combination of shares or other change affecting such outstanding Common Stock as
a class without receipt of consideration, then appropriate adjustments shall be
made by the Plan Administrator to (i) the class and maximum number of shares
issuable over the term of this Plan, (ii) the class and maximum number of shares
purchasable per Participant during each Offering Period, (iii) the class and
maximum number of shares purchasable in the aggregate by all Participants on any
one purchase date under the Plan and (iv) the class and number of shares and the
price per share of the Common Stock subject to each purchase right at the time
outstanding under this Plan. Such adjustments shall be designed to preclude the
dilution or enlargement of rights and benefits under this Plan.

7. Purchase Rights.

(a) Terms and Conditions. An Employee who participates in this Plan for a
particular Offering Period shall have the right to purchase shares of Common
Stock during such Offering

 

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Number reflects the one-for-four reverse stock split effected June 8, 2006 (with
the original 4,000,000 shares issuable under the Plan becoming 1,000,000 shares)
plus additional shares added thereafter.

 

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Period, upon the terms and conditions set forth below and shall execute a
subscription agreement embodying such terms and conditions and such other
provisions (not inconsistent with the Plan) as the Plan Administrator may deem
advisable.

(b) Purchase Price. Common Stock shall be issuable at the end of each Offering
Period at a purchase price equal to the lower of (i) 85% of the fair market
value per share on the Participant’s Enrollment Date for such Offering Period or
(ii) the fair market value per share on the date on which such Offering Period
ends, provided, however, that for the first Offering Period the purchase price
will be equal to the lower of (i) 85% of the fair market value per share on the
date of shareholder approval of the Plan or (ii) the fair market value per share
on the date on which the first Offering Period ends.

(c) Valuation. For purposes of determining the fair market value per share of
Common Stock on any relevant date, the following procedures shall be in effect:

(i) The fair market value on any date shall be equal to the closing price of the
Common Stock on such date, as reported in The Wall Street Journal or other
comparable sources. If there is no quoted price for such date, then the closing
price on the next preceding day for which there does exist such a quotation, as
so reported, shall be determinative of fair market value.

(ii) If Section 7(c)(1) is not applicable, the fair market value shall be
determined by the Plan Administrator in good faith. Such determination shall be
conclusive and binding on all persons.

(d) Number of Purchasable Shares. The number of shares purchasable per
Participant for each Offering Period shall be the number of whole shares
obtained by dividing the amount collected from the Participant through payroll
deductions during such Offering Period by the purchase price in effect for the
Offering Period. No Participant, however, may purchase shares in violation of
Section 8(a).

(e) Payment. Payment for the Common Stock purchased under the Plan shall be
effected only by means of the Participant’s authorized payroll deductions. Such
deductions shall begin on the first day coincident with or immediately following
the Participant’s Enrollment Date into the Offering Period and shall continue
through the pay period ending with or immediately prior to the last day of the
Offering Period. The amounts so collected shall be credited to the Participant’s
book account under the Plan, but no interest shall be paid on the balance from
time to time outstanding in such account. The amounts collected from a
Participant

 

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may be commingled with the general assets of the Company and may be used for
general corporate purposes.

(f) Termination of Purchase Right. The following provisions shall govern the
termination of outstanding purchase rights:

(i) A Participant may terminate his or her payroll deductions in a current
Offering Period by filing a withdrawal form with the Plan Administrator at least
10 business days prior to the payroll period for which it is to be effective.
The Participant will not receive the funds then accumulated in his or her
account, and any such funds will be applied to the purchase of shares at the end
of such Offering Period. If such withdrawal is filed at least 10 business days
prior to the beginning of the next Offering Period, then such withdrawal will
constitute a termination of participation in the Plan with respect to such
successive Offering Periods as contemplated by Section 7(f)(ii).

(ii) A Participant may terminate his or her participation in the Plan with
respect to the next successive Offering Period by filing, at any time prior to
10 business days before the commencement of the next successive Offering Period,
the prescribed notification form with the Plan Administrator (or its designate).
No payroll deductions shall be collected from the Participant with respect to
the terminated purchase right for such successive Offering Period.

(iii) The withdrawal and termination of such purchase right shall be
irrevocable, and the Participant may not subsequently rejoin the Offering Period
for which such withdrawn or terminated purchase right was granted. In order to
resume participation in any subsequent Offering Period, such individual must
re-enroll in the Plan by making a timely filing of a new subscription agreement
and payroll withholding authorization.

(iv) If the Participant ceases to remain an Eligible Employee while his/her
purchase right remains outstanding and within 3 months prior to the end of the
current Offering Period, then such individual (or the personal representative of
the estate of a deceased Participant) shall have the following election,
exercisable until 10 business days prior to the end of the Offering Period in
which the Participant ceases Eligible Employee status:

(1) to withdraw all of the Participant’s payroll deductions for such Offering
Period, without interest, or

(2) to have such funds held for the purchase of shares at the end of the
Offering Period in which his or her status as an Eligible Employee ceased.

 

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If no such election is made, or if no such election is available because the
Participant ceased to be an Eligible Employee at a time that is 3 months or more
prior to the end of the current Offering Period, then such funds shall be
refunded, without interest, as soon as possible after the close of such Offering
Period. In no event, however, may any payroll deductions be made on the
Participant’s behalf following his/her cessation of Eligible Employee status.

(g) Stock Purchase. Shares of Common Stock shall automatically be purchased on
behalf of each Participant at the end of each Offering Period and for all
purposes shares of Common Stock purchased pursuant to the Plan shall be deemed
to have been issued and sold at the close of business on the last date of each
Offering Period. The purchase shall be effected by applying such Participant’s
payroll deductions for the Offering Period to the purchase of whole shares of
Common Stock (subject to the limitation on the maximum number of purchasable
shares) at the purchase price in effect for such Offering Period. Any payroll
deductions not applied to such purchase because they are not sufficient to
purchase a whole share shall be carried over for application in the successive
Offering Period unless the Participant has withdrawn from the Plan, in which
event such amount will be refunded to the Participant, without interest.

(h) Proration of Purchase Rights. Subject to the limitations set forth in
Section 6(a), the Plan Administrator may determine the number of shares of
Common Stock, subject to periodic adjustment under Section 6(b), which may be
purchased in the aggregate by all Participants in any one Offering Period under
the Plan. Should the total number of shares of Common Stock which are to be
purchased pursuant to outstanding purchase rights on any particular date exceed
either (i) the maximum limitation on the number of shares purchasable in the
aggregate on such date or (ii) the number of shares then available for issuance
under the Plan, the Plan Administrator shall make a pro rata allocation of the
available shares on a uniform and nondiscriminatory basis, and the payroll
deductions of each Participant, to the extent in excess of the aggregate
purchase price payable for the Common Stock prorated to such individual, shall
be refunded to such Participant, without interest.

(i) Rights as Shareholder. A Participant shall have no rights as a shareholder
with respect to the shares subject to his/her outstanding purchase right until
the shares are actually purchased on the Participant’s behalf in accordance with
the applicable provisions of the Plan. No adjustments shall be made for
dividends, distributions or other rights for which the record date is prior to
the date of such purchase.

A Participant shall be entitled to receive, as soon as practicable after each
Offering Period, a stock certificate for the number of shares purchased on the
Participant’s behalf. Such

 

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certificate may, upon the Participant’s request, be issued in the names of the
Participant and his/her spouse as tenants-in-common or as joint tenants with
right of survivorship.

(j) Assignability. Purchase rights granted under this Plan shall not be
assignable or transferable by the Participant other than by will or by the laws
of descent and distribution following the Participant’s death, shall not be
subject to execution, attachment or similar process, and shall be exercised
during the Participant’s lifetime only by the Participant.

(k) Change in Ownership. Should the Company or its shareholders enter into an
agreement to dispose of all or substantially all of the assets or outstanding
capital stock of the Company by means of:

(i) a sale, merger or other reorganization in which the Company will not be the
surviving corporation (other than a reorganization effected primarily to change
the state in which the Company is incorporated), or

(ii) a reverse merger in which the Company is the surviving corporation but in
which more than 50% of the Company’s outstanding voting stock is transferred to
holders different from those who held the stock immediately prior to the reverse
merger, then, unless the successor shall continue this Plan and assume all the
obligations evidenced by the outstanding rights to purchase shares of Common
Stock or shall provide equivalent rights with respect to the successor’s
securities, all to the reasonable satisfaction of the Board, all outstanding
purchase rights under the Plan shall automatically be exercised immediately
prior to the consummation of such sale, merger, reorganization or reverse merger
by applying the payroll deductions of each Participant for the Offering Period
in which such transaction occurs to the purchase of whole shares of Common Stock
at the lower of (i) 85% of the fair market value of the Common Stock on the
Participant’s Enrollment Date into the Offering Period in which such transaction
occurs or (ii) the fair market value of the Common Stock immediately prior to
the consummation of such transaction. However, the applicable share limitations
of Sections 7 and 8 shall continue to apply to any such purchase.

The Company shall use its best efforts to provide at least 10 days’ advance
written notice of the occurrence of any such sale, merger, reorganization or
reverse merger, and Participants shall, following the receipt of such notice,
have the right to terminate their outstanding purchase rights in accordance with
the applicable provisions of this Sections 7.

 

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8. Accrual Limitations.

(a) Dollar Limit. No Participant shall be entitled to accrue rights to acquire
Common Stock pursuant to any purchase right outstanding under this Plan if and
to the extent such accrual, when aggregated with rights to purchase Common Stock
accrued under any other purchase right outstanding under this Plan and similar
rights accrued under other employee stock purchase plans (within the meaning of
Section 423 of the Code) of the Company, would otherwise permit such Participant
to purchase more than $25,000 worth of stock of the Company (determined on the
basis of the fair market value of such stock on the date or dates such rights
are granted to the Participant) for each calendar year such rights are at any
time outstanding.

(b) Application. For purposes of applying such accrual limitations, the right to
acquire Common Stock pursuant to each purchase right outstanding under the Plan
shall accrue as follows:

(i) No right to acquire Common Stock under any outstanding purchase right shall
accrue to the extent the Participant has already accrued in the same calendar
year the right to acquire $25,000 worth of Common Stock (determined on the basis
of the fair market value on the date or dates of grant) pursuant to one or more
purchase rights held by the Participant during such calendar year.

(ii) If by reason of such accrual limitations, any purchase right of a
Participant does not accrue for a particular Offering Period, then the payroll
deductions which the Participant made during that Offering Period with respect
to such purchase right shall be refunded, without interest.

(c) Controlling Provision. In the event there is any conflict between the
provisions of this Section 8 and one or more provisions of the Plan or any
instrument issued thereunder, the provisions of this Section 8 shall be
controlling.

9. Status of Plan Under Federal Tax Laws.

This Plan is designed to qualify as an employee stock purchase plan under Code
Section 423, and shall be governed and construed accordingly.

10. Amendment and Termination.

 

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(a) Amendments, Suspension, Discontinuation. The Board may alter, amend, suspend
or discontinue this Plan immediately following the close of any Offering Period.
However, the Board may not, without the approval of the Company’s shareholders:

(i) materially increase the number of shares issuable under this Plan or the
maximum number of shares which may be purchased per Participant or in the
aggregate during any one Offering Period under this Plan, except that the Plan
Administrator shall have the authority, exercisable without such shareholder
approval, to effect adjustments to the extent necessary to effect changes in the
Company’s capital structure pursuant to Section 6(b);

(ii) alter the purchase price formula so as to reduce the purchase price payable
for the shares of Common Stock issuable under this Plan;

(iii) materially increase the benefits accruing to Participants under the Plan
or materially modify the requirements for eligibility to participate in this
Plan; or

(iv) adopt amendments which require shareholder approval under applicable law,
including Section 16(b) of the Securities Exchange Act of 1934.

(b) Termination of Purchase Rights. The Company shall have the right,
exercisable in the sole discretion of the Plan Administrator, to terminate all
outstanding purchase rights under this Plan immediately following the close of
any Offering Period. Should the Company elect to exercise such right, then this
Plan shall terminate in its entirety. No further purchase rights shall
thereafter be granted or exercised, and no further payroll deductions shall
thereafter be collected, under this Plan.

11. General Provisions.

(a) Requirements. No shares of Common Stock shall be issued hereunder, including
any additional shares of Common Stock added to the Plan pursuant to
Section 10(a)(i), until (i) this Plan, or any additional shares of Common Stock,
as applicable, shall have been approved by the Company’s shareholders and
(ii) the Company shall have complied with all relevant provisions of law,
including, without limitation, any applicable state securities laws, the
Securities Act of 1933, as amended, the Securities Exchange Act of 1934, as
amended, the rules and regulations promulgated thereunder, applicable laws of
foreign countries and other jurisdictions, the requirements of any quotation
service or stock exchange upon which the shares may then be listed, and all
other applicable requirements established by law or regulation.

 

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(b) Plan Termination. This Plan shall terminate upon the earlier of
(i) September 30, 2016 or (ii) the date on which all shares available for
issuance under the Plan shall have been sold pursuant to purchase rights
exercised under this Plan. In the event shareholder approval is not obtained, or
such legal compliance is not effected, within 12 months after the date on which
the Plan is adopted by the Board, or amended by the Board such that shareholder
approval is required, the Plan shall terminate and have no further force or
effect, and all funds collected by the Company following the non-approval of the
Plan or amendment, as applicable, shall be returned to all subscribers, without
interest; provided, however, that no additional shares of Common Stock that have
been added to the Plan pursuant to Section 10(a)(i) shall be issued to an
Eligible Employee until shareholder approval, if required, is obtained.

(c) Costs. All costs and expenses incurred in the administration of this Plan
shall be paid by the Company.

(d) No Status as Employee. Neither the action of the Company in establishing the
Plan, or any action taken under this Plan by the Board or the Plan
Administrator, nor any provision of this Plan itself shall be construed so as to
grant any person the right to remain in the employ of the Company for any period
of specific duration, and such person’s employment may be terminated at any
time, with or without cause.

(e) No Segregation of Funds. All payroll deductions received or held by the
Company under this Plan may be used by the Company for any corporate purposes
and the Company shall not be obligated to segregate the payroll deductions.

(f) No Interest. No Participant shall be entitled, at any time, to any payment
or credit for interest with respect to or on the payroll deductions contemplated
herein, or on any other assets held hereunder for the Participant’s account.

(g) Governing Law. The provisions of this Plan shall be governed by the laws of
the State of Washington.

 

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