<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:


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         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


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                  otherwise defined herein are used as defined in the
                  Transaction Documents




               [THE REMAINDER OF THIS PAGE IS INTENTIONALLY BLANK]


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                       [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>


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<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


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