Document:

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                                                                     Exhibit 4.4

                          REGISTRATION RIGHTS AGREEMENT

                  THIS REGISTRATION RIGHTS AGREEMENT, dated as of November 6,
2001, between the investor or investors signatory hereto (each an "Investor" and
together the "Investors"), and Cray Inc., a Washington corporation (the
"Company").

                  WHEREAS, simultaneously with the execution and delivery of
this Agreement, the Investors are purchasing from the Company, pursuant to the
Convertible Subordinated Debentures and Warrants Purchase Agreement dated the
date hereof (the "Purchase Agreement") (capitalized terms not defined herein
shall have the meanings ascribed to them in the Purchase Agreement), $8,000,000,
in the aggregate, principal amount of the Company's 5% Convertible Subordinated
Debentures and Warrants; and

                  WHEREAS, the Company desires to grant to the Investors the
registration rights set forth herein with respect to the Conversion Shares of
Common Stock issuable upon conversion of, or as interest upon, the Convertible
Subordinated Debentures, shares of Common Stock issuable upon exercise of the
Warrants purchased pursuant to the Purchase Agreement and shares issuable in the
event of a registration default pursuant to Section 2(f) (the "Securities").

                  NOW, THEREFORE, the parties hereto mutually agree as follows:

                  Section 1. Restrictions on Transfer. Each Investor
acknowledges and understands that prior to the registration of the Securities as
provided herein, the Securities are "restricted securities" as defined in Rule
144 promulgated under the Securities Act. Each Investor understands that no
disposition or transfer of the Securities may be made by Investor in the absence
of (i) an opinion of counsel to the Investor, in form and substance reasonably
satisfactory to the Company, that such transfer may be made without registration
under the Securities Act, or (ii) such registration.

                           With a view to making available to the Investors the
benefits of Rule 144 under the Securities Act or any other similar rule or
regulation of the Commission that may at any time permit the Investors to sell
securities of the Company to the public without registration ("Rule 144"), the
Company agrees to:

                  (a) comply with the provisions of paragraph (c)(1) of Rule
         144;

                  (b) file with the Commission in a timely manner all reports
         and other documents required to be filed with the Commission pursuant
         to Section 13 or 15(d) under the Exchange Act by companies subject to
         either of such sections, irrespective of whether the Company is then
         subject to such reporting requirements; and

                  (c) upon request by the Transfer Agent, the Company shall
         promptly provide the Transfer Agent an opinion of counsel, which
         opinion shall be reasonably acceptable to
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         the Transfer Agent, that the Investor has complied with the applicable
         conditions of Rule 144 (or any similar provision then in force) under
         the Securities Act.

 .1.               Section 2. Registration Rights With Respect to the Securities.

                  (a) The Company agrees that it will prepare and file with the
         Commission, within 30 calendar days after the Closing Date, a
         registration statement on Form S-3, or another registration statement
         (on Form S-1, or other appropriate registration statement form) under
         the Securities Act (as applicable, the "Registration Statement"), at
         the sole expense of the Company (except as provided in Section 2(c)
         hereof), in respect of the Investors, so as to permit the resale of the
         Securities under the Act by the Investors as selling stockholders and
         not as underwriters.

                  (b) The Company shall cause such Registration Statement to
         become effective within 90 calendar days (120 calendar days in the
         event of a "full review" by the SEC) after the Closing Date, or, if
         earlier, within 5 Trading Days of SEC clearance to request acceleration
         of effectiveness. The number of shares designated in the Registration
         Statement to be registered shall include all the Warrant Shares, 100%
         of the already converted Conversion Shares held by any Investor on the
         filing date and at least 200% of the greater of the number of shares
         which would be issuable upon the conversion of the principal amount of
         the Convertible Subordinated Debentures issued and to be issued at the
         Conversion Price in effect (i) on the Closing Date, or (ii) on the date
         of the filing of the Registration Statement, and such number of shares
         as the Company deems prudent for the purpose of issuing shares of
         Common Stock as interest on the Convertible Subordinated Debentures,
         and shall include appropriate language regarding reliance upon Rule 416
         to the extent permitted by the Commission. The Company will notify the
         Investors and its transfer agent of the effectiveness of the
         Registration Statement within 1 Trading Day of such event. After the
         Effective Date, within 20 days after the day on which the number of
         Securities registered for resale by the Investors, notwithstanding the
         limitation on conversion herein and in the Purchase Agreement, is less
         than 125% of the number of Securities (calculated at the Conversion
         Price on such date) held by the Investors on such date (the "Further
         Registration Date"), the Company shall file a further registration
         statement registering a number of shares of Common Stock to the extent
         that at least 200% of the shares which would be required to be issued
         upon the conversion of the remaining Convertible Subordinated
         Debentures at the Conversion Price on the date of the filing of such
         further registration statement are registered and shall prosecute such
         additional registration statement to effectiveness within 90 calendar
         days of the date of the Further Registration Date (120 calendar days in
         the event of a "full review" of such additional registration statement
         by the SEC). Each Investor shall have the right to convert all or any
         of its Convertible Subordinated Debenture into up to a number of
         registered shares of Common Stock equal to such Investor's fraction of
         the aggregate Purchase Price multiplied by the initially registered
         and, if applicable, subsequently registered Securities; provided,
         however, in no event shall this provision limit each Investor's right
         to convert its Convertible Subordinated Debenture into unregistered
         Common Stock.

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                  (c) The Company will maintain the Registration Statement or
         post-effective amendment filed under this Section 2 effective under the
         Securities Act until the earliest of (i) the date that none of the
         Securities covered by such Registration Statement are or may become
         issued and outstanding, (ii) the date that all of the Securities have
         been sold pursuant to such Registration Statement, (iii) the date the
         Investors receive an opinion of counsel to the Company, which counsel
         shall be reasonably acceptable to the Investors, that the Securities
         may be sold under the provisions of Rule 144 without limitation as to
         volume, (iv) all Securities have been otherwise transferred to persons
         who may trade such shares without restriction under the Securities Act,
         and the Company has delivered a new certificate or other evidence of
         ownership for such securities not bearing a restrictive legend, or (v)
         three (3) years from the Effective Date.

                  (d) All fees, disbursements and out-of-pocket expenses and
         costs incurred by the Company in connection with the preparation and
         filing of the Registration Statement hereunder and in complying with
         applicable securities and Blue Sky laws (including, without limitation,
         all attorneys' fees of the Company) shall be borne by the Company. The
         Investors shall bear the cost of underwriting and/or brokerage
         discounts, fees and commissions, if any, applicable to the Securities
         being registered and the fees and expenses of their counsel. The
         Investors and their counsel shall have a reasonable period, not to
         exceed 5 Trading Days, to review the proposed Registration Statement or
         any amendment thereto, prior to filing with the Commission, and the
         Company shall provide each Investor with copies of any comment letters
         received from the Commission with respect thereto within 2 Trading Days
         of receipt thereof. The Company shall qualify any of the securities for
         sale in such states as any Investor reasonably designates and shall
         furnish indemnification in the manner provided in Section 5 hereof.
         However, the Company shall not be required to qualify in any state
         which will require an escrow or other restriction relating to the
         Company and/or the sellers, or which will require the Company to
         qualify to do business in such state or require the Company to file
         therein any general consent to service of process. The Company at its
         expense will supply the Investors with copies of the applicable
         Registration Statement and the prospectus included therein and other
         related documents in such quantities as may be reasonably requested by
         the Investors.

                  (e) The Company shall not be required by this Section 2 to
         include an Investor's Registrable Securities in any Registration
         Statement which is to be filed if, in the opinion of counsel for both
         the Investor and the Company (or, should they not agree, in the opinion
         of another counsel experienced in securities law matters acceptable to
         counsel for the Investor and the Company) the proposed offering or
         other transfer as to which such registration is requested is exempt
         from applicable federal and state securities laws and would result in
         all purchasers or transferees obtaining securities which are not
         "restricted securities", as defined in Rule 144 under the Securities
         Act.

                  (f) In the event that (i) the Registration Statement is not
         filed by the Company in a timely manner as set forth in Section 2(a),
         (ii) the Registration Statement is not

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         declared effective by the Commission within the period of time set
         forth in Section 2(b) herein, or within five (5) Trading Days of
         clearance by the Commission to request effectiveness, (iii) such
         Registration Statement is not maintained as effective by the Company
         for the period set forth in Section 2(c) above, or (iv) the additional
         registration statement referred to in Section 2(b) is not filed within
         20 calendar days or declared effective within 90 or, if applicable, 120
         calendar days as set forth therein (each a "Registration Default") then
         the Company will pay each Investor (pro-rata on a monthly basis), for
         each Registration Default then in effect, as liquidated damages and not
         as a penalty, during any period in which a Registration Default is
         occurring, two percent (2%) per month of (i) the then outstanding
         principal amount of the Convertible Subordinated Debentures, and (ii)
         the value of any outstanding Warrants (valued at the difference between
         the average closing bid price during the applicable month and the
         Exercise Price multiplied by the number of Warrant Shares the Warrants
         are exercisable into), held by such Investor until such corresponding
         Registration Default no longer exists ("Liquidated Damages"). Such
         payment of the Liquidated Damages shall be made to the Investors in
         cash, or, at the option of the Company, in registered shares of Common
         Stock (based on the Conversion Price (as defined in the Convertible
         Subordinated Debenture)) on the Trading Day prior to the date of
         payment) on the last day of each month during which a Registration
         Default occurred or was continuing, without demand therefor by the
         Investor; provided, however, that the payment of the Liquidated Damages
         shall not relieve the Company from its obligations to register the
         Securities pursuant to this Section.

                  If the Company does not remit the payment to the Investors as
         set forth above, the Company will pay the Investors reasonable costs of
         collection, including attorneys' fees, in addition to the Liquidated
         Damages and interest of 15% per annum on any liquidated damage payments
         not made in a timely manner as set forth above. The registration of the
         Securities pursuant to this provision shall not affect or limit the
         Investors' other rights or remedies as set forth in this Agreement.

                  (g) The Company shall be precluded from including in any
         registration statement which it is required to file pursuant to this
         Section 2 any other securities apart from the Registrable Securities,
         without the prior written consent of a majority in interest of the
         Investors.

                  (h) If at any time or from time to time after the effective
         date of any Registration Statement, the Company notifies the Investors
         in writing of the existence of a Potential Material Event (as defined
         in Section 2(i) below), the Investors shall not offer or sell any
         Securities or engage in any other transaction involving or relating to
         Securities, from the time of the giving of notice with respect to a
         Potential Material Event until the Investors receive written notice
         from the Company that such Potential Material Event either has been
         disclosed to the public or no longer constitutes a Potential Material
         Event; provided, however, that the Company may not so suspend the right
         to such holders of Securities for more than twenty-five (25) calendar
         days in the aggregate during any twelve month period (the "Blackout
         Period"), during the period the Registration

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         Statement is required to be in effect (such 25 day calendar period
         including any preclusion pursuant to Section 3(f)), and if such period
         is exceeded, such event shall be a Registration Default and subject to
         liquidated damages as set forth in Section 2(f) hereof. THE COMPANY
         MUST GIVE THE INVESTORS NOTICE IN WRITING PRIOR TO THE FIRST DAY OF THE
         BLACKOUT PERIOD AS PROMPTLY AS PRACTICABLE AFTER BECOMING AWARE THAT
         SUCH A BLACKOUT PERIOD (WITHOUT INDICATING THE NATURE OF SUCH BLACKOUT
         PERIOD) WILL OCCUR AND SUCH NOTICE MUST BE ACKNOWLEDGED IN WRITING BY
         THE INVESTORS. FAILURE TO PROVIDE THE INVESTORS WITH SUCH NOTICE SHALL
         CONSTITUTE A REGISTRATION DEFAULT DURING THE ENTIRE APPLICABLE PERIOD
         THAT THE REGISTRATION STATEMENT IS SUSPENDED. Compliance by the Company
         with this Section 2(h) will not result in or be deemed a breach of any
         of the Company's obligations set forth in the Purchase Agreement not to
         disclose non-public information to the Investors.

                  (i) "Potential Material Event" means any of the following: (a)
         the possession by the Company of material information not ripe for
         disclosure in a registration statement, as determined in good faith by
         the Chief Executive Officer or the Board of Directors of the Company
         that disclosure of such information in a Registration Statement would
         be detrimental to the business and affairs of the Company; or (b) any
         material engagement or activity by the Company which would, in the good
         faith determination of the Chief Executive Officer or the Board of
         Directors of the Company, be adversely affected by disclosure in a
         registration statement at such time, which determination shall be
         accompanied by a good faith determination by the Chief Executive
         Officer or the Board of Directors of the Company that the applicable
         Registration Statement would be materially misleading absent the
         inclusion of such information.

                  Section 3. Cooperation with Company. The Investors will
cooperate with the Company in all respects in connection with this Agreement,
including timely supplying all information reasonably requested by the Company
(which shall include all information regarding the Investors and proposed manner
of sale of the Registrable Securities required to be disclosed in any
Registration Statement) and executing and returning all documents reasonably
requested in connection with the registration and sale of the Registrable
Securities and entering into and performing their obligations under any
underwriting agreement, if the offering is an underwritten offering, in usual
and customary form, with the managing underwriter or underwriters of such
underwritten offering. Nothing in this Agreement shall obligate any Investor to
consent to be named as an underwriter in any Registration Statement. The
obligation of the Company to register the Registrable Securities shall be
absolute and unconditional as to those Securities which the Commission will
permit to be registered without naming the Investors as underwriters. Any delay
or delays caused by the Investors by failure to cooperate as required hereunder
shall not constitute a Registration Default.

                  Section 4. Registration Procedures. If and whenever the
Company is required by any of the provisions of this Agreement to effect the
registration of any of the Registrable Securities under the Act, the Company
shall (except as otherwise provided in this Agreement), as expeditiously as
possible, subject to the Investors' assistance and cooperation as reasonably
required with respect to each Registration Statement:

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                  (a) (i) prepare and file with the Commission such amendments
         and supplements to the Registration Statement and the prospectus used
         in connection therewith as may be necessary to keep such Registration
         Statement effective and to comply with the provisions of the Act with
         respect to the sale or other disposition of all Registrable Securities
         covered by such Registration Statement whenever the Investors shall
         desire to sell or otherwise dispose of the same (including prospectus
         supplements with respect to the sales of Registrable Securities from
         time to time in connection with a registration statement pursuant to
         Rule 415 promulgated under the Act) and (ii) take all lawful action
         such that each of (A) the Registration Statement and any amendment
         thereto does not, when it becomes effective, contain an untrue
         statement of a material fact or omit to state a material fact required
         to be stated therein or necessary to make the statements therein, in
         light of the circumstances under which they were made, not misleading
         and (B) the prospectus forming part of the Registration Statement, and
         any amendment or supplement thereto, does not at any time during the
         Registration Period include an untrue statement of a material fact or
         omit to state a material fact required to be stated therein or
         necessary to make the statements therein, in light of the circumstances
         under which they were made, not misleading;

                  (b) (i) prior to the filing with the Commission of any
         Registration Statement (including any amendments thereto) and the
         distribution or delivery of any prospectus (including any supplements
         thereto), provide draft copies thereof to the Investors as required by
         Section 2(d) and reflect in such documents all such comments as the
         Investors (and their counsel) reasonably may propose respecting the
         Selling Shareholders and Plan of Distribution sections (or
         equivalents); (ii) furnish to each Investor such numbers of copies of a
         prospectus including a preliminary prospectus or any amendment or
         supplement to any prospectus, as applicable, in conformity with the
         requirements of the Act, and such other documents, as such Investor may
         reasonably request in order to facilitate the public sale or other
         disposition of the Registrable Securities owned by such Investor; and
         (iii) provide to each Investor copies of any comments and
         communications from the Commission relating to the Registration
         Statement, if lawful to do so;

                  (c) register and qualify the Registrable Securities covered by
         the Registration Statement under such other securities or blue sky laws
         of such jurisdictions as the Investors shall reasonably request
         (subject to the limitations set forth in Section 2(d) above), and do
         any and all other acts and things which may be necessary or advisable
         to enable each Investor to consummate the public sale or other
         disposition in such jurisdiction of the Registrable Securities owned by
         such Investor;

                  (d) list such Registrable Securities on the Principal Market,
         if the listing of such Registrable Securities is then permitted under
         the rules of such Principal Market;

                  (e) notify each Investor at any time when a prospectus
         relating thereto covered by the Registration Statement is required to
         be delivered under the Act, of the happening of any event of which it
         has knowledge as a result of which the prospectus included in the

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         Registration Statement, as then in effect, includes an untrue statement
         of a material fact or omits to state a material fact required to be
         stated therein or necessary to make the statements therein not
         misleading in the light of the circumstances then existing, subject to
         Section 2(h), other than a Potential Material Event, and the Company
         shall prepare and file a curative amendment under Section 4(a) as
         quickly as commercially possible and during such period, the Investors
         shall not make any sales of Registrable Securities pursuant to the
         Registration Statement and during such period; provided, however, any
         period during which the Investors are precluded from making sales of
         the Registrable Securities shall be included in the 25 calendar day
         period in Section 2(h) and any such days herein which exceed, or cause
         the Company to exceed, such 25 calendar day period shall be deemed a
         Registration Default and the Company shall be subject to Liquidated
         Damages as set forth in Section 2(f).

                  (f) as promptly as practicable after becoming aware of such
         event, notify each Investor who holds Registrable Securities being sold
         (or, in the event of an underwritten offering, the managing
         underwriters) of the issuance by the Commission of any stop order or
         other suspension of the effectiveness of the Registration Statement at
         the earliest possible time and take all lawful action to effect the
         withdrawal, recession or removal of such stop order or other
         suspension;

                  (g) cooperate with the Investors to facilitate the timely
         preparation and delivery of certificates for the Registrable Securities
         to be offered pursuant to the Registration Statement and enable such
         certificates for the Registrable Securities to be in such denominations
         or amounts, as the case may be, as the Investors reasonably may request
         and registered in such names as the Investors may request; and, within
         3 Trading Days after a Registration Statement which includes
         Registrable Securities is declared effective by the Commission, deliver
         and cause legal counsel selected by the Company to deliver to the
         transfer agent for the Registrable Securities (with copies to the
         Investors) an appropriate instruction and, to the extent necessary, an
         opinion of such counsel;

                  (h) take all such other lawful actions reasonably necessary to
         expedite and facilitate the disposition by the Investors of their
         Registrable Securities in accordance with the intended methods therefor
         provided in the prospectus which are customary for issuers to perform
         under the circumstances;

                  (i) in the event of an underwritten offering, promptly include
         or incorporate in a prospectus supplement or post-effective amendment
         to the Registration Statement such information as the managers
         reasonably agree should be included therein and to which the Company
         does not reasonably object and make all required filings of such
         prospectus supplement or post-effective amendment as soon as
         practicable after it is notified of the matters to be included or
         incorporated in such Prospectus supplement or post-effective amendment;
         and

                  (j) maintain a transfer agent and registrar for its Common
         Stock.

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                  Section 5.  Indemnification.

                  (a) To the maximum extent permitted by law, the Company agrees
         to indemnify and hold harmless the Investors and each person, if any,
         who controls an Investor within the meaning of the Securities Act (each
         a "Distributing Investor") against any losses, claims, damages or
         liabilities, joint or several (which shall, for all purposes of this
         Agreement, include, but not be limited to, all reasonable costs of
         defense and investigation and all reasonable attorneys' fees and
         expenses), to which the Distributing Investor may become subject, under
         the Securities Act or otherwise, insofar as such losses, claims,
         damages or liabilities (or actions in respect thereof) arise out of or
         are based upon any untrue statement or alleged untrue statement of any
         material fact contained in any Registration Statement, or any related
         final prospectus or amendment or supplement thereto, or arise out of or
         are based upon the omission or alleged omission to state therein a
         material fact required to be stated therein or necessary to make the
         statements therein not misleading; provided, however, that the Company
         will not be liable in any such case to the extent, and only to the
         extent, that any such loss, claim, damage or liability arises out of or
         is based upon an untrue statement or alleged untrue statement or
         omission or alleged omission made in such Registration Statement,
         preliminary prospectus, final prospectus or amendment or supplement
         thereto in reliance upon, and in conformity with, written information
         furnished to the Company by the Distributing Investor, its counsel,
         affiliates or any underwriter, specifically for use in the preparation
         thereof or (ii) by such Investor's failure to deliver to the purchaser
         a copy of the most recent prospectus (including any amendments or
         supplements thereto. This indemnity agreement will be in addition to
         any liability, which the Company may otherwise have.

                  (b) To the maximum extent permitted by law, each Distributing
         Investor agrees that it will indemnify and hold harmless the Company,
         and each officer and director of the Company or person, if any, who
         controls the Company within the meaning of the Securities Act, against
         any losses, claims, damages or liabilities (which shall, for all
         purposes of this Agreement, include, but not be limited to, all
         reasonable costs of defense and investigation and all reasonable
         attorneys' fees and expenses) to which the Company or any such officer,
         director or controlling person may become subject under the Securities
         Act or otherwise, insofar as such losses, claims, damages or
         liabilities (or actions in respect thereof) arise out of or are based
         upon any untrue statement or alleged untrue statement of any material
         fact contained in any Registration Statement, or any related final
         prospectus or amendment or supplement thereto, or arise out of or are
         based upon the omission or the alleged omission to state therein a
         material fact required to be stated therein or necessary to make the
         statements therein not misleading, but in each case only to the extent
         that such untrue statement or alleged untrue statement or omission or
         alleged omission was made in such Registration Statement, final
         prospectus or amendment or supplement thereto in reliance upon, and in
         conformity with, written information furnished to the Company by such
         Distributing Investor, its counsel, affiliates or any underwriter,
         specifically for use in the preparation thereof. This indemnity
         agreement will be in addition to any liability, which the Distributing
         Investor may otherwise have. Notwithstanding anything to the contrary
         herein, the Distributing

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         Investor shall be liable under this Section 5(b) for only that amount
         as does not exceed the net proceeds to such Distributing Investor as a
         result of the sale of Registrable Securities pursuant to the
         Registration Statement.

                  (c) Promptly after receipt by an indemnified party under this
         Section 5 of notice of the commencement of any action against such
         indemnified party, such indemnified party will, if a claim in respect
         thereof is to be made against the indemnifying party under this Section
         5, notify the indemnifying party in writing of the commencement
         thereof; but the omission so to notify the indemnifying party will not
         relieve the indemnifying party from any liability which it may have to
         any indemnified party except to the extent the failure of the
         indemnified party to provide such written notification actually
         prejudices the ability of the indemnifying party to defend such action.
         In case any such action is brought against any indemnified party, and
         it notifies the indemnifying party of the commencement thereof, the
         indemnifying party will be entitled to participate in, and, to the
         extent that it may wish, jointly with any other indemnifying party
         similarly notified, assume the defense thereof, subject to the
         provisions herein stated and after notice from the indemnifying party
         to such indemnified party of its election so to assume the defense
         thereof, the indemnifying party will not be liable to such indemnified
         party under this Section 5 for any legal or other expenses subsequently
         incurred by such indemnified party in connection with the defense
         thereof other than reasonable costs of investigation, unless the
         indemnifying party shall not pursue the action to its final conclusion.
         The indemnified parties as a group shall have the right to employ one
         separate counsel in any such action and to participate in the defense
         thereof, but the fees and expenses of such counsel shall not be at the
         expense of the indemnifying party if the indemnifying party has assumed
         the defense of the action with counsel reasonably satisfactory to the
         indemnified party unless (i) the employment of such counsel has been
         specifically authorized in writing by the indemnifying party, or (ii)
         the named parties to any such action (including any impleaded parties)
         include both the indemnified party and the indemnifying party and the
         indemnified party shall have been advised by its counsel that there may
         be one or more legal defenses available to the indemnifying party
         different from or in conflict with any legal defenses which may be
         available to the indemnified party or any other indemnified party (in
         which case the indemnifying party shall not have the right to assume
         the defense of such action on behalf of such indemnified party, it
         being understood, however, that the indemnifying party shall, in
         connection with any one such action or separate but substantially
         similar or related actions in the same jurisdiction arising out of the
         same general allegations or circumstances, be liable only for the
         reasonable fees and expenses of one separate firm of attorneys for the
         indemnified party, which firm shall be designated in writing by the
         indemnified party). No settlement of any action against an indemnified
         party shall be made without the prior written consent of the
         indemnified party, which consent shall not be unreasonably withheld so
         long as such settlement includes a full release of claims against the
         indemnified party.

                  All fees and expenses of the indemnified party (including
         reasonable costs of defense and investigation in a manner not
         inconsistent with this Section and all

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         reasonable attorneys' fees and expenses) shall be paid to the
         indemnified party, as incurred, within ten (10) Trading Days of written
         notice thereof to the indemnifying party; provided, that the
         indemnifying party may require such indemnified party to undertake to
         reimburse all such fees and expenses to the extent it is finally
         judicially determined that such indemnified party is not entitled to
         indemnification hereunder.

                  Section 6. Contribution. In order to provide for just and
equitable contribution under the Securities Act in any case in which (i) the
indemnified party makes a claim for indemnification pursuant to Section 5 hereof
but is judicially determined (by the entry of a final judgment or decree by a
court of competent jurisdiction and the expiration of time to appeal or the
denial of the last right of appeal) that such indemnification may not be
enforced in such case notwithstanding the fact that the express provisions of
Section 5 hereof provide for indemnification in such case, or (ii) contribution
under the Securities Act may be required on the part of any indemnified party,
then the Company and the applicable Distributing Investor shall contribute to
the aggregate losses, claims, damages or liabilities to which they may be
subject (which shall, for all purposes of this Agreement, include, but not be
limited to, all reasonable costs of defense and investigation and all reasonable
attorneys' fees and expenses), in either such case (after contribution from
others) on the basis of relative fault as well as any other relevant equitable
considerations. The relative fault shall be determined by reference to, among
other things, whether the untrue or alleged untrue statement of a material fact
or the omission or alleged omission to state a material fact relates to
information supplied by the Company on the one hand or the applicable
Distributing Investor on the other hand, and the parties' relative intent,
knowledge, access to information and opportunity to correct or prevent such
statement or omission. The Company and the Distributing Investor agree that it
would not be just and equitable if contribution pursuant to this Section 6 were
determined by pro rata allocation or by any other method of allocation which
does not take account of the equitable considerations referred to in this
Section 6. The amount paid or payable by an indemnified party as a result of the
losses, claims, damages or liabilities (or actions in respect thereof) referred
to above in this Section 6 shall be deemed to include any legal or other
expenses reasonably incurred by such indemnified party in connection with
investigating or defending any such action or claim. No person guilty of
fraudulent misrepresentation (within the meaning of Section 11(f) of the
Securities Act) shall be entitled to contribution from any person who was not
guilty of such fraudulent misrepresentation.

         Notwithstanding any other provision of this Section 6, in no event
shall any (i) Investor be required to undertake liability to any person under
this Section 6 for any amounts in excess of the dollar amount of the proceeds
received by such Investor from the sale of such Investor's Registrable
Securities (after deducting any fees, discounts and commissions applicable
thereto) pursuant to any Registration Statement under which such Registrable
Securities are registered under the Securities Act and (ii) underwriter be
required to undertake liability to any person hereunder for any amounts in
excess of the aggregate discount, commission or other compensation payable to
such underwriter with respect to the Registrable Securities underwritten by it
and distributed pursuant to such Registration Statement.

                                       10
<PAGE>
                  Section 7. Notices. All notices, demands, requests, consents,
approvals, and other communications required or permitted hereunder shall be in
writing and, unless otherwise specified herein, shall be (i) hand delivered,
(ii) deposited in the mail, registered or certified, return receipt requested,
postage prepaid, (iii) delivered by reputable air courier service with charges
prepaid, or (iv) transmitted by facsimile, addressed as set forth in the
Purchase Agreement or to such other address as such party shall have specified
most recently by written notice. Any notice or other communication required or
permitted to be given hereunder shall be deemed effective (a) upon hand delivery
or delivery by facsimile, with accurate confirmation generated by the
transmitting facsimile machine, at the address or number designated below (if
delivered on a business day during normal business hours where such notice is to
be received), or the first business day following such delivery (if delivered
other than on a business day during normal business hours where such notice is
to be received) or (b) on the first business day following the date of sending
by reputable courier service, fully prepaid, addressed to such address, or (c)
upon actual receipt of such mailing, if mailed. Either party hereto may from
time to time change its address or facsimile number for notices under this
Section 7 by giving at least ten (10) days' prior written notice of such changed
address or facsimile number to the other party hereto.

                  Section 8. Assignment. This Agreement is binding upon and
inures to the benefit of the parties hereto and their respective heirs,
successors and permitted assigns. The rights granted the Investors under this
Agreement may be assigned to any purchaser of substantially all of the
Registrable Securities (or the rights thereto) from an Investor, as otherwise
permitted by the Purchase Agreement.

                  Section 9. Additional Covenants of the Company. The Company
agrees that, for so long as it shall be required to maintain the effectiveness
of the Registration Statement, it shall file all reports and information
required to be filed by it with the Commission in a timely manner and take all
such other action so as to maintain such eligibility for the use of such form.

                  Section 10. Counterparts/Facsimile. This Agreement may be
executed in two or more counterparts, each of which shall constitute an
original, but all of which, when together shall constitute but one and the same
instrument, and shall become effective when one or more counterparts have been
signed by each party hereto and delivered to the other parties. In lieu of the
original, a facsimile transmission or copy of the original shall be as effective
and enforceable as the original.

                  Section 11. Remedies. The remedies provided in this Agreement
are cumulative and not exclusive of any remedies provided by law. If any term,
provision, covenant or restriction of this Agreement is held by a court of
competent jurisdiction to be invalid, illegal, void or unenforceable, the
remainder of the terms, provisions, covenants and restrictions set forth herein
shall remain in full force and effect and shall in no way be affected, impaired
or invalidated, and the parties hereto shall use their best efforts to find and
employ an alternative means to achieve the same or substantially the same result
as that contemplated by such term, provision, covenant or restriction.

                                       11
<PAGE>
                  Section 12. Conflicting Agreements. The Company shall not
enter into any agreement with respect to its securities that is inconsistent
with the rights granted to the holders of Registrable Securities in this
Agreement or otherwise prevents the Company from complying with all of its
obligations hereunder.

                  Section 13. Headings. The headings in this Agreement are for
reference purposes only and shall not affect in any way the meaning or
interpretation of this Agreement.

                  Section 14. Governing Law. This Agreement shall be governed by
and construed in accordance with the laws of the State of New York applicable to
contracts made in New York by persons domiciled in New York City and without
regard to its principles of conflicts of laws. The Company and each of the
Investors agree to submit themselves to the in personam jurisdiction of the
state and federal courts situated within the Southern District of the State of
New York with regard to any controversy arising out of or relating to this
Agreement. The non-prevailing party to any dispute hereunder shall pay the
expenses of the prevailing party, including reasonable attorneys' fees, in
connection with any such dispute.

             [THE REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK.]

                                       12
<PAGE>
                [SIGNATURE PAGE TO REGISTRATION RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have caused this Registration Rights
Agreement to be duly executed as of the date first written above.

                                   CRAY INC.

                                   By: /s/
                                       -----------------------------------------
                                           James E. Rottsolk, Chairman

                                   INVESTORS:

                                   RIVERVIEW GROUP, LLC

                                   By: /s/
                                       -----------------------------------------
                                   Name:   Terry Feeney
                                   Title:  Chief Administrative Officer

                                   OMICRON PARTNERS, LP
                                   By:  Omicron Capital L.P., as subadvisor
                                   By:  Omicron Capital Inc., it general partner

                                   By: /s/
                                       -----------------------------------------
                                           Olivier Morali, President

                                   LATERMAN & CO.

                                   By: /s/
                                       -----------------------------------------
                                           Bernard Laterman, Managing Partner

                                   FOREVERGREEN PARTNERS

                                   By: /s/
                                       -----------------------------------------
                                           Bernard Laterman, Managing Partner

                                       13<PAGE>
                                                                     Exhibit 4.5
                               AMENDMENT NO. 1 TO
                       CONVERTIBLE SUBORDINATED DEBENTURES
                                       AND
                           WARRANT PURCHASE AGREEMENT
                         AND OTHER TRANSACTION DOCUMENTS

         THIS AMENDMENT NO. 1 TO THE CONVERTIBLE SUBORDINATED DEBENTURES AND
WARRANT PURCHASE AGREEMENT AND OTHER TRANSACTION DOCUMENTS, dated as of November
15, 2001, is by and between the Investors (as such term is defined below) and
Cray Inc., a corporation organized and existing under the laws of the State of
Washington (the "Company").

         WHEREAS, the Company and Riverview Group, LLC, Omicron Partners, LP,
Laterman & Co. and Forevergreen Partners (together, the "Original Investors")
are parties to a Convertible Subordinated Debentures and Warrant Purchase
Agreement, dated as of November 6, 2001 (the "Purchase Agreement") pursuant to
which the Original Investors invested $8,000,000 in the Company in return for an
aggregate of $8,000,000 principal amount of Convertible Subordinated Debentures
(the "Debentures") and Warrants (the "Warrants") to purchase an aggregate of
316,206 shares of the Company's Common Stock, $.01 par value per share (the
"Common Stock"), and

         WHEREAS, Clarion Capital Corporation and Morton A. Cohen TTEE FBO The
Morton A. Cohen Revocable Living Trust (together, the "New Investors") wish to
invest an aggregate of $1,300,000 in the Company on the same terms as the
Original Investors (the "Investment"), and the Original Investors desire that
the New Investors so invest in the Company,

         WHEREAS, the Company and the Original Investors executed and delivered
the Purchase Agreement and a Registration Rights Agreement (together, the
"Transaction Documents")

         NOW THEREFOR, in consideration of the foregoing premises, and the
promises and covenants herein contained, the receipt and sufficiency of which
are hereby acknowledged by the parties hereto, the parties, intending to be
legally bound, hereby agree as follows:

         1.       Amendment to Transaction Documents. The parties hereto hereby
                  amend each of the Transaction Documents as follows:

                                       1
<PAGE>
         a)       the total principal amount of the Debentures will be
                  $9,300,000, with an aggregate of $1,300,000 principal amount
                  of the Debentures being issued to the New Investors;

         b)       the total Warrants to be issued will cover an aggregate of
                  367,590 shares of Common Stock, with an aggregate of Warrants
                  for 51,384 shares of Common Stock being issued to the New
                  Investors; and

         c)       to add the New Investors as parties thereto to the full extent
                  and as if they were original parties to each of the
                  Transaction Documents, with the Company and the New Investors
                  making the same representations and warranties to each other
                  and agreeing to bound by the same covenants as contained in
                  each of the Transaction Documents.

         d)       the Company agrees that to forever surrender its right to
                  redeem the Debentures held by the Original Investors and the
                  New Investors pursuant to an Optional Redemption Notice (as
                  defined therein) in Section 5 of the Debentures or otherwise
                  exercise any rights it may have to force the Original
                  Investors or the New Investors to convert their Debentures
                  other than pursuant to Section 4(b) of the Debentures,
                  provided, however, that this provision will not alter or
                  restrict any rights the Original Investors or the New
                  Investors have under the Purchase Agreement or Debentures to
                  cause the Company to redeem the Debentures pursuant to the
                  terms therein.

         2.       Debentures and Warrants. The principal amount of the
                  Debentures and the number of Warrant Shares being received by
                  each of the New Investors are set forth on the signature page
                  hereof.

         3.       Consent and Waivers. The Original Investors hereby consent to
                  the investment by the New Investors and waive the provisions
                  of Section 5.9 of the Purchase Agreement with respect to the
                  Investment only, and also agree that the issuance of the
                  Debentures and the Warrants to the New Investors and the
                  issuance of the shares of Common Stock under the Debentures
                  and upon exercise of the Warrants will be exempt from the
                  anti-dilution provisions of Section 4(e) of the Debentures.

         4.       Closing. The Company acknowledges the receipt of $1,300,000
                  from the New Investors and the New Investors hereby
                  acknowledge receipt of the Debentures and Warrants.

         5.       Definitions. The term "Investors" is defined to include both
                  the Original Investors and the New Investors. All capitalized
                  terms not

                                       2
<PAGE>
                  otherwise defined herein are used as defined in the
                  Transaction Documents

               [THE REMAINDER OF THIS PAGE IS INTENTIONALLY BLANK]

                                       3
<PAGE>
                       [Signature Page to Amendment No. 1]

         IN WITNESS WHEREOF, the parties hereto have caused this Amendment No. 1
to be executed by the undersigned, thereunto duly authorized, as of the date
first written above.

<TABLE>
<S>                                            <C>
                                               CRAY INC.

                                                        /S/
                                               By

                                                     James E. Rottsolk, Chairman

                                               NEW INVESTORS

                                               CLARION CAPITAL CORPORATION

                                                        /S/
                                               By

                                                      Morton A. Cohen, President
Address for Notice:
1801 East Ninth Street, Suite 1120
Cleveland, Ohio  44144
Fax: 216-694-3545
$1,000,000 principal amount of Debentures and
39,526 Warrant Shares

                                               MORTON A. COHEN TTEE FBO
                                               THE MORTON A COHEN REVOCABLE
                                               LIVING TRUST

                                                        /S/
                                               By

                                                        Morton A. Cohen, Trustee

Address for Notice:
1801 East Ninth Street, Suite 1120
Cleveland, Ohio  44144
Fax: 216-694-3545
$300,000 principal amount of Debentures and
11,858 Warrant Shares
</TABLE>

                                       4
<PAGE>
                                   OLD INVESTORS

                                   RIVERVIEW GROUP, LLC

                                        /S/
                                   By

                                        Name:  Terry Feeney
                                        Title:    Chief Administrative Officer

                                   OMICRON PARTNERS, LP
                                   By:  Omicron Capital L.P., as subadvisor
                                   By:  Omicron Capital Inc., general partner

                                        /S/
                                   By:
                                        Olivier Morali, President

                                   LATERMAN &. CO.

                                        /S/
                                   By

                                        Bernard Laterman, Managing Partner

                                   FOREVERGREEN PARTNERS

                                        /S/
                                   By

                                        Bernard Laterman, Managing Partner

                                       5

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