<PAGE>   1

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                UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                             ---------------------

                                  FORM 10-K/A


                               (AMENDMENT NO. 2)


     [X]         ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

                  FOR THE FISCAL YEAR ENDED SEPTEMBER 30, 2000

     [ ]       TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

             FOR THE TRANSITION PERIOD FROM           TO

                             ---------------------

                         COMMISSION FILE NUMBER 0-21484
                         THE SANTA CRUZ OPERATION, INC.
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                            <C>
                 CALIFORNIA                                     94-2549086
        (State or other jurisdiction                         (I.R.S. Employer
      of incorporation or organization)                     Identification No.)

             400 ENCINAL STREET,
           SANTA CRUZ, CALIFORNIA                                  95060
  (Address of principal executive offices)                      (Zip Code)
</TABLE>

       Registrant's telephone number, including area code (831) 425-7222

        Securities Registered Pursuant to Section 12(b) of the Act: NONE

          Securities Registered Pursuant to Section 12(g) of the Act:
           Preferred Share Purchase Rights Common Stock, No Par Value

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days.  Yes [X]  No [ ]

     Registrant became subject to such filing requirements on May 25, 1993 as a
result of its initial public offering.

     Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to
contained to the best of registrant's knowledge, in definitive proxy or
information statements incorporated by reference in Part III of this Form 10-K
or any amendment to this Form 10-K.  [ ]

     The aggregate market value of the voting stock held by non-affiliates of
the registrant, based upon the closing sale price of the Common Stock on
November 1, 2000 as reported on the Nasdaq National Market was approximately
$4.0938 Shares of Common Stock held by each executive officer and director and
by each person who owns 5% or more of the outstanding Common Stock have been
excluded in that such persons may be deemed to be affiliates. This determination
of affiliate status is not necessarily a conclusive determination for other
purposes.

     As of November 1, 2000, registrant had 39,441,763 shares of Common Stock
outstanding.
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<PAGE>   2

                                    PART IV

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULE AND REPORTS ON FORM 8-K

     (a) Documents filed as part of Form 10-K

  1. Financial Statement Schedule

<TABLE>
<CAPTION>
        SCHEDULE                                                    PAGE
         NUMBER                         DESCRIPTION                NUMBER
        --------                        -----------                ------
<S>                       <C>                                      <C>
           II                Valuation and Qualifying Accounts       26
</TABLE>

     The independent auditors' reports with respect to the above-listed
financial statement schedule appears on page 25 of this report on Form 10-K.
Financial statement schedules other than those listed above have been omitted
since they are either not required, not applicable, or the information is shown
in the financial statements or notes thereto.

  2. Exhibit Listing

<TABLE>
<CAPTION>
        EXHIBIT
         NUMBER                                  DESCRIPTION
        -------                                  -----------
<C>                      <S>
          2.0            -- Asset Purchase Agreement By and Between The Santa Cruz
                            Operation, Inc. and Novell, Inc.(4)
          3.1            -- Restated Articles of Incorporation of Registrant.(2)
          3.2            -- Bylaws of Registrant, as amended.(5)
          4.1            -- Specimen Common Stock Certificate of Registrant.(1)
         10.11           -- Software License Agreement with Locus Computing
                            Corporation effective January 11, 1989.(1)
         10.12           -- Lease with Encinal Partnership No. 1 commencing May 1,
                            1991 (100 Pioneer Street).(1)
         10.13           -- Lease with Encinal Partnership No. 1 commencing January
                            1, 1989 (425 Encinal Street).(1)
         10.14           -- Lease with Wave Crest Development, Inc. commencing August
                            1, 1987 (440 Encinal Street).(1)
         10.15           -- Lease with Wave Crest Development, Inc. commencing June
                            1, 1988 (400 Encinal Street).(1)
         10.16           -- Lease with Wave Crest Development, Inc. commencing July
                            1, 1988 (399 Encinal Street).(1)
         10.17           -- Form of Indemnification Agreement.(1)
         10.18           -- Master Registration Rights Agreement as amended.(1)
         10.19           -- 1993 Stock Purchase Plan and form of Stock Purchase
                            Agreement.(3)(8)
</TABLE>

<PAGE>   3


<TABLE>
<CAPTION>
        EXHIBIT
         NUMBER                                  DESCRIPTION
        -------                                  -----------
<C>                      <S>
         10.20           -- 1994 Incentive Stock Option Plan and form of Incentive
                            Stock Option Agreement.(3)(8)
         10.21           -- 401(k) Plan, as amended.(1)(8)
         10.23           -- Revised 1993 Employee Stock Purchase Plan.(5)(8)
         10.24           -- 1993 Director Stock Option Plan.(1)(8)
         10.34           -- Shareholders' Rights Agreement.(6)
         10.35           -- Change-in-control agreement between the Company and
                            certain key management.(8)
         10.36           -- Employment Agreement with Alok Mohan.(7)
         21.1            -- Subsidiaries of Registrant.(9)
         23.1            -- Consent of Independent Accountants.
         27.1            -- Financial Data Schedule.(9)
</TABLE>


---------------

(1) Incorporated by reference to Registration Statement 33-60548 on Form S-1.

(2) Incorporated by reference to the Form 10-K filed on December 24, 1993.

(3) Incorporated by reference to the Form 10-K filed on December 23, 1994.

(4) Incorporated by reference to the Form 8-K filed on December 20, 1995.

(5) Incorporated by reference to the Form 10-K filed on December 22, 1995.

(6) Incorporated by reference to the Form 8-A12G filed on September 18, 1997.

(7) Incorporated by reference to the Form 10-K filed on December 23, 1998.

(8) Designates management contracts or compensatory plans, contracts or
    arrangements.


(9) Incorporated by reference to the Amendment No. 1 to Form 10-K filed on
    March 23, 2002.


     (b) Reports on Form 8-K.

     On September 22, 2000, the Company filed a Current Report on Form 8-K to
report that the Company had entered into an agreement to sell 409,375 units as
$32.00. A unit consists of eight shares of common stock of the Company and a
warrant to purchase either two additional shares of the Company's common stock
at $4.00 per share or one share of the common stock of Caldera held by the
Company at $8.00 per share. The warrants for the Caldera shares can be exercised
only if the Agreement between the Company and Caldera is consummated.

<PAGE>   4

                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15 (d) of the Securities
Exchange Act of 1934, the registrant has duly caused this Annual Report to be
signed on its behalf by the undersigned, thereunto duly authorized.

                                               THE SANTA CRUZ OPERATION, INC.


<TABLE>
<S>                                            <C>
           By: /s/ RANDALL BRESEE                        By: /s/ STEVEN M. SABBATH
---------------------------------------------  ---------------------------------------------
               Randall Bresee                                Steven M. Sabbath
           Senior Vice President,                         Senior Vice President,
           Chief Financial Officer                 Law and Corporate Affairs & Secretary

            Date: March 26, 2001                           Date: March 26, 2001
</TABLE>





     Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
registrant and in the capacities and on the dates indicated:


<TABLE>
<CAPTION>
NAME                                                                TITLE                    DATE
----                                                                -----                    ----
<C>                                                      <S>                            <C>

                         *                               President, Chief Executive     March 26, 2001
-----------------------------------------------------      Officer and Director
                 Douglas L. Michels

                         *                               Chairman of the Board of       March 26, 2001
-----------------------------------------------------      Directors
                     Alok Mohan

                         *                               Director                       March 26, 2001
-----------------------------------------------------
                Gilbert P. Williamson

                         *                               Director                       March 26, 2001
-----------------------------------------------------
                   Ronald Lachman

                         *                               Director                       March 26, 2001
-----------------------------------------------------
                  Robert M. McClure

                         *                               Director                       March 26, 2001
-----------------------------------------------------
                  R. Duff Thompson

                         *                               Director                       March 26, 2001
-----------------------------------------------------
                    Ninian Eadie
</TABLE>



* By:          /s/ STEVEN M. SABBATH
     -------------------------------------------------
                   Steven M. Sabbath
                   Attorney-in-fact

<PAGE>   5

                               INDEX TO EXHIBITS

<TABLE>
<CAPTION>
        EXHIBIT
         NUMBER                                  DESCRIPTION
        -------                                  -----------
<C>                      <S>
          2.0            -- Asset Purchase Agreement By and Between The Santa Cruz
                            Operation, Inc. and Novell, Inc.(4)
          3.1            -- Restated Articles of Incorporation of Registrant.(2)
          3.2            -- Bylaws of Registrant, as amended.(5)
          4.1            -- Specimen Common Stock Certificate of Registrant.(1)
         10.11           -- Software License Agreement with Locus Computing
                            Corporation effective January 11, 1989.(1)
         10.12           -- Lease with Encinal Partnership No. 1 commencing May 1,
                            1991 (100 Pioneer Street).(1)
         10.13           -- Lease with Encinal Partnership No. 1 commencing January
                            1, 1989 (425 Encinal Street).(1)
         10.14           -- Lease with Wave Crest Development, Inc. commencing August
                            1, 1987 (440 Encinal Street).(1)
         10.15           -- Lease with Wave Crest Development, Inc. commencing June
                            1, 1988 (400 Encinal Street).(1)
         10.16           -- Lease with Wave Crest Development, Inc. commencing July
                            1, 1988 (399 Encinal Street).(1)
         10.17           -- Form of Indemnification Agreement.(1)
         10.18           -- Master Registration Rights Agreement as amended.(1)
         10.19           -- 1993 Stock Purchase Plan and form of Stock Purchase
                            Agreement.(3)(8)
         10.20           -- 1994 Incentive Stock Option Plan and form of Incentive
                            Stock Option Agreement.(3)(8)
         10.21           -- 401(k) Plan, as amended.(1)(8)
         10.23           -- Revised 1993 Employee Stock Purchase Plan.(5)(8)
         10.24           -- 1993 Director Stock Option Plan.(1)(8)
         10.34           -- Shareholders' Rights Agreement.(6)
         10.35           -- Change-in-control agreement between the Company and
                            certain key management.(8)
         10.36           -- Employment Agreement with Alok Mohan.(7)
         21.1            -- Subsidiaries of Registrant.(9)
         23.1            -- Consent of Independent Accountants.
         27.1            -- Financial Data Schedule.(9)
</TABLE>

---------------

(1) Incorporated by reference to Registration Statement 33-60548 on Form S-1.

(2) Incorporated by reference to the Form 10-K filed on December 24, 1993.

(3) Incorporated by reference to the Form 10-K filed on December 23, 1994.

(4) Incorporated by reference to the Form 8-K filed on December 20, 1995.

(5) Incorporated by reference to the Form 10-K filed on December 22, 1995.

(6) Incorporated by reference to the Form 8-A12G filed on September 18, 1997.

(7) Incorporated by reference to the Form 10-K filed on December 23, 1998.

(8) Designates management contracts or compensatory plans, contracts or
    arrangements.


(9) Incorporated by reference to the Amendment No. 1 to Form 10-K filed on
    March 23, 2001.