<PAGE>   1

        AMENDMENT NO. 2 TO FORM 10-Q FOR PERIOD ENDED SEPTEMBER 30, 1998
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D. C. 20549


                                  FORM 10-Q/A
                                Amendment No. 2

(MARK ONE)

[X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES AND
    EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDING SEPTEMBER 30, 1998

                                       OR
[ ] TRANSACTION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES AND
    EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM _____ TO ______
                         Commission File Number 0-24457

                             BEYOND.COM CORPORATION
                  (formerly known as Software.net Corporation)
          (Exact name of Registrant as specified in its charter)

<TABLE>
<S>                                                  <C>
           Delaware                                                94-3212136
    (State of Incorporation)                         (IRS Employer Identification Number)

3200 Patrick Henry Drive, Santa Clara, California                     95054
(Address of principal executive offices)                            (Zip Code)
</TABLE>

Registrant's Telephone Number, including Area Code: (408) 855-3000

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
                                  ---      ---

The number of shares outstanding of each of the issuer's classes of common stock
as of September 30, 1998:

<TABLE>
<S>                                                           <C>
                  Class                                    Number of Shares
Common Stock, par value $0.001                                27,334,744
</TABLE>

<PAGE>   2

     The Registrant hereby amends the disclosure contained in Part II, Item 6 of
the Registrant's Quarterly Report on Form 10-Q/A, Amendment No. 1 for the period
ended September 30, 1998 and to add information in Part II, Item 6. The complete
text of such item, as amended, follows.

<PAGE>   3

PART II.  OTHER INFORMATION

          ITEM 6. Exhibits and Reports on Form 8-K

                  (a)  EXHIBITS.

<TABLE>
<CAPTION>
                  EXHIBIT
                  NUMBER                 DESCRIPTION
                  -------                -----------
                  <S>          <C>
                  10.1*        Agreement dated as of September 11, 1998, by and
                               between the Registrant and the United States
                               National Imaging and Mapping Agency ( NIMA
                               Contract # N00140-98-D-2139)
                  10.2         Co-hosting Agreement dated as of September 21,
                               1998, by and between the Registrant and Network
                               Associates, Inc.
                  10.3         Web Site Service Agreement dated as of September 21, 1998,
                               by and between the Registrant and Network Associates, Inc.
                  10.4         Electronic Services Distribution Agreement dated as of
                               September 1, 1997, by and between The Registrant and McAfee
                               Software, Inc.
                  27.1*        Financial Data Schedule

</TABLE>


*Previously filed as an exhibit to this Registration Statement.
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                                   SIGNATURES

     Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


                                        Beyond.com Corporation
                                        f/k/a/ Software.net Corporation
                                        (Registrant)




DATE: August 3, 2000                    BY: /s/ Curtis A. Cluff
                                           ------------------------------------
                                            Curtis A. Cluff
                                            Senior Vice President and
                                            Chief Financial Officer

<PAGE>   5

                               INDEX TO EXHIBITS


<TABLE>
<CAPTION>
Exhibit
Number                             Description
-------                            -----------
<S>          <C>
10.2         Co-hosting Agreement dated as of September 21, 1998, by and between
             the Registrant and Network Associates, Inc.

10.3         Web Site Service Agreement dated as of September 21, 1998, by and
             between the Registrant and Network Associates, Inc.

10.4         Electronic Services Distribution Agreement dated as of September 1,
             1997, by and between The Registrant and McAfee Software, Inc.
</TABLE>