<PAGE>   1
                                                                    EXHIBIT 4.13

                            BROADBASE SOFTWARE, INC.
                         NON-PLAN STOCK OPTION AGREEMENT


               This Stock Option Agreement (this "AGREEMENT") is made and
entered into as of the date of grant set forth below (the "DATE OF GRANT") by
and between Broadbase Software, Inc., a Delaware corporation (the "COMPANY"),
and the optionee named below ("OPTIONEE"). Capitalized terms not defined herein
shall have the meaning ascribed to them in Section 20.

OPTIONEE:                             Rusty Thomas
SOCIAL SECURITY NUMBER:
                                      -------------------------------
OPTIONEE'S ADDRESS:
                                      -------------------------------

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

TOTAL OPTION SHARES:                  175,000
EXERCISE PRICE PER SHARE:             $54.00
DATE OF GRANT:                        1/4/2000
VESTING START DATE:                   1/4/2000
EXPIRATION DATE:                      1/4/2010
TYPE OF STOCK OPTION:                 Nonqualified Stock Option

        1. GRANT OF OPTION. The Company hereby grants to Optionee an option
(this "OPTION") to purchase up to the total number of shares of common stock of
the Company, $0.001 par value ("COMMON STOCK"), set forth above (collectively,
the "SHARES") at the Exercise Price Per Share set forth above (the "EXERCISE
PRICE"), subject to all of the terms and conditions of this Agreement.

        2. VESTING; EXERCISE PERIOD.

               2.1 Vesting of Shares. This Option shall be exercisable as it
vests. Subject to the terms and conditions of this Agreement, this Option shall
vest and become exercisable as to portions of the Shares as follows: (a) this
Option shall not be exercisable with respect to any of the Shares until April 4,
2000 (the "FIRST VESTING DATE"); (b) if Optionee has continuously provided
services to the Company, or any Parent or Subsidiary of the Company, then on the
First Vesting Date, this Option shall become exercisable as to 6.25% of the
Shares; and (c) thereafter this Option shall become exercisable as to an
additional 2.083% of the Shares on each monthly anniversary of the First Vesting
Date, provided that Optionee has continuously provided services to the Company,
or any Parent or Subsidiary of the Company. Furthermore, in the event of a
change in control of at least 50% of the voting stock of the company, in
conjunction with the optionee not being offered to continue in the same
position, then 50% of your unvested shares shall immediately vest. This Option
shall cease to vest upon Optionee's


<PAGE>   2
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

Termination and Optionee shall in no event be entitled under this Option to
purchase a number of shares of the Company's Common Stock greater than the
"Total Option Shares."

               2.2 Expiration. This Option shall expire on the Expiration Date
set forth above and must be exercised, if at all, on or before the earlier of
the Expiration Date or the date on which this Option is earlier terminated in
accordance with the provisions of Section 3, provided, however, that this Option
will be not be exercisable after the expiration of ten (10) years from the Date
of Grant.

        3. TERMINATION.

               3.1 Termination for Any Reason Except Death, Disability or Cause.
If Optionee is Terminated for any reason except Optionee's death, Disability or
Cause, then this Option, to the extent (and only to the extent) that it is
vested in accordance with the schedule set forth in Section 2.1 of this
Agreement on the date of Termination, may be exercised by Optionee no later than
three (3) months after the date of Termination, but in any event no later than
the Expiration Date.

               3.2 Termination Because of Death or Disability. If Optionee is
Terminated because of death or Disability of Optionee (or the Optionee dies
within three (3) months after a Termination other than because of death,
Disability or Cause), then this Option, to the extent that it is vested in
accordance with the schedule set forth in Section 2.1 of this Agreement on the
date of Termination, may be exercised by Optionee (or Optionee's legal
representative) no later than twelve (12) months after the date of Termination,
but in any event no later than the Expiration Date.

               3.3 Termination for Cause. If Optionee is Terminated for Cause,
this Option will expire on the Optionee's date of Termination.

               3.4 No Obligation to Employ. Nothing in this Agreement shall
confer on Optionee any right to continue in the employ of, or other relationship
with, the Company or any Parent or Subsidiary of the Company, or limit in any
way the right of the Company or any Parent or Subsidiary of the Company to
terminate Optionee's employment or other relationship at any time, with or
without Cause.

        4. MANNER OF EXERCISE.

               4.1 Stock Option Exercise Agreement. To exercise this Option,
Optionee (or in the case of exercise after Optionee's death, Optionee's
executor, administrator, heir or legatee, as the case may be) must deliver to
the Company an executed stock option exercise agreement in the form attached
hereto as Exhibit A, or in such other form as may be approved by the Company
from time to time (the "EXERCISE AGREEMENT"), which shall set forth, inter alia,
Optionee's election to exercise this Option, the number of shares being
purchased, any restrictions imposed on the Shares and any representations,
warranties and agreements regarding


                                      -3-


<PAGE>   3
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

Optionee's investment intent and access to information as may be required by the
Company to comply with applicable securities laws. If someone other than
Optionee exercises this Option, then such person must submit documentation
reasonably acceptable to the Company that such person has the right to exercise
this Option.

               4.2 Limitations on Exercise. This Option may not be exercised
unless such exercise is in compliance with all applicable federal and state
securities laws, as they are in effect on the date of exercise. This Option may
not be exercised as to fewer than 100 Shares unless it is exercised as to all
Shares as to which this Option is then exercisable.

               4.3 Payment. The Exercise Agreement shall be accompanied by full
payment of the Exercise Price for the Shares being purchased in cash (by check),
or where permitted by law:

        (a)     provided that a public market for the Company's stock exists:
                (1) through a "same day sale" commitment from Optionee and a
                broker-dealer that is a member of the National Association of
                Securities Dealers (an "NASD DEALER") whereby Optionee
                irrevocably elects to exercise this Option and to sell a portion
                of the Shares so purchased to pay for the exercise price and
                whereby the NASD Dealer irrevocably commits upon receipt of such
                Shares to forward the exercise price directly to the Company; or
                (2) through a "margin" commitment from Optionee and -- a NASD
                Dealer whereby Optionee irrevocably elects to exercise this
                Option and to pledge the Shares so purchased to the NASD Dealer
                in a margin account as security for a loan from the NASD Dealer
                in the amount of the exercise price, and whereby the NASD Dealer
                irrevocably commits upon receipt of such Shares to forward the
                exercise price directly to the Company; or

        (b)     by any combination of the foregoing.

               4.4 Tax Withholding. Prior to the issuance of the Shares upon
exercise of this Option, Optionee must pay or provide for any applicable federal
or state withholding obligations of the Company. If the Committee permits,
Optionee may provide for payment of withholding taxes upon exercise of this
Option by requesting that the Company retain Shares with a Fair Market Value
equal to the minimum amount of taxes required to be withheld. In such case, the
Company shall issue the net number of Shares to the Optionee by deducting the
Shares retained from the Shares issuable upon exercise.

               4.5 Issuance of Shares. Provided that the Exercise Agreement and
payment are in form and substance satisfactory to counsel for the Company, the
Company shall issue the Shares registered in the name of Optionee, Optionee's
authorized assignee, or Optionee's legal representative, and shall deliver
certificates representing the Shares with the appropriate legends affixed
thereto.

        5. COMPLIANCE WITH LAWS AND REGULATIONS. The exercise of this Option and


                                      -4-


<PAGE>   4
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

the issuance and transfer of Shares shall be subject to compliance by the
Company and Optionee with all applicable requirements of federal and state
securities laws and with all applicable requirements of any stock exchange on
which the Company's Common Stock may be listed at the time of such issuance or
transfer. Optionee understands that the Company is under no obligation to
register or qualify the Shares with the Securities and Exchange Commission, any
state securities commission or any stock exchange to effect such compliance.

        6. NONTRANSFERABILITY OF OPTION. This Option may not be transferred in
any manner other than by will or by the laws of descent and distribution and may
be exercised during the lifetime of Optionee only by Optionee. The terms of this
Option shall be binding upon the executors, administrators, successors and
assigns of Optionee.

        7. TAX CONSEQUENCES. Set forth below is a brief summary of some of the
federal and California tax consequences of exercise of this Option and
disposition of the Shares. THIS SUMMARY IS NECESSARILY INCOMPLETE, AND THE TAX
LAWS AND REGULATIONS ARE SUBJECT TO CHANGE. OPTIONEE SHOULD CONSULT A TAX
ADVISOR BEFORE EXERCISING THE OPTION OR DISPOSING OF THE SHARES.

               7.1 Exercise of Nonqualified Stock Option. There may be a regular
federal and California income tax liability upon the exercise of this Option.
Optionee will be treated as having received compensation income (taxable at
ordinary income tax rates) equal to the excess, if any, of the fair market value
of the Shares on the date of exercise over the Exercise Price. The Company will
be required to withhold from Optionee's compensation or collect from Optionee
and pay to the applicable taxing authorities an amount equal to a percentage of
this compensation income at the time of exercise.

               7.2 Disposition of Shares. If the Shares are held for more than
twelve (12) months after the date of the transfer of the Shares pursuant to the
exercise of an NQSO, any gain realized on disposition of the Shares will be
treated as long-term capital gain, as the case may be.

        8. PRIVILEGES OF STOCK OWNERSHIP. Optionee shall not have any of the
rights of a shareholder with respect to any Shares until Optionee exercises this
Option and pays the Exercise Price.

        9. INTERPRETATION. Any dispute regarding the interpretation of this
Agreement shall be submitted by Optionee or the Company to the Committee for
review. The resolution of such a dispute by the Committee shall be final and
binding on the Company and Optionee.

        10. ENTIRE AGREEMENT. This Agreement and the Exercise Agreement
constitute the entire agreement and understanding of the parties hereto with
respect to the subject matter hereof and supersede all prior understandings and
agreements with respect to such subject matter.

        11. NOTICES. Any notice required to be given or delivered to the Company


                                      -5-


<PAGE>   5
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

under the terms of this Agreement shall be in writing and addressed to the
Corporate Secretary of the Company at its principal corporate offices. Any
notice required to be given or delivered to Optionee shall be in writing and
addressed to Optionee at the address indicated above or to such other address as
such party may designate in writing from time to time to the Company. All
notices shall be deemed to have been given or delivered upon: personal delivery;
three (3) days after deposit in the United States mail by certified or
registered mail (return receipt requested); one (1) business day after deposit
with any return receipt express courier (prepaid); or one (1) business day after
transmission by rapifax or telecopier.

        12. SUCCESSORS AND ASSIGNS. The Company may assign any of its rights
under this Agreement. This Agreement shall be binding upon and inure to the
benefit of the successors and assigns of the Company. Subject to the
restrictions on transfer set forth herein, this Agreement shall be binding upon
Optionee and Optionee's heirs, executors, administrators, legal representatives,
successors and assigns.

        13. GOVERNING LAW. This Agreement shall be governed by and construed in
accordance with the internal laws of the State of California, without regard to
that body of law pertaining to choice of law or conflict of law.

        14. ACCEPTANCE. Optionee hereby acknowledges receipt of a copy of this
Agreement. Optionee has read and understands the terms and provisions thereof,
and accepts this Option subject to all the terms and conditions of this
Agreement. Optionee acknowledges that there may be adverse tax consequences upon
exercise of this Option or disposition of the Shares and that the Company has
advised Optionee to consult a tax advisor prior to such exercise or disposition.

        15. MODIFICATION, EXTENSION OR RENEWAL. The Committee may modify, extend
or renew this Option and authorize the grant of new options in substitution
therefor, provided that any such action may not, without the written consent of
the Optionee, impair any of such Optionee's rights under this Option. The
Committee may reduce the Exercise Price of this Option without the consent of
the Optionee affected by a written notice to them; provided, however, that the
Exercise Price may not be reduced below 85% of the Fair Market Value of the
Shares on the date of grant.

        16. CERTIFICATES. All certificates for Shares or other securities
delivered upon exercise of this Option will be subject to such stock transfer
orders, legends and other restrictions as the Committee may deem necessary or
advisable, including restrictions under any applicable federal, state or foreign
securities law, or any rules, regulations and other requirements of the SEC or
any stock exchange or automated quotation system upon which the Shares may be
listed or quoted.

        17. ADJUSTMENT OF SHARES. In the event that the number of outstanding
shares is changed by a stock dividend, recapitalization, stock split, reverse
stock split, subdivision, combination, reclassification or similar change in the
capital structure of the Company without


                                      -6-


<PAGE>   6
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

consideration, then the Exercise Price of and the number of Shares subject to
this Option will be proportionately adjusted, subject to any required action by
the Board or the Optionee and compliance with applicable securities laws;
provided, however, that fractions of a Share will not be issued but will either
be replaced by a cash payment equal to the Fair Market Value of such fraction of
a Share or will be rounded up to the nearest whole Share, as determined by the
Committee.

        18. CORPORATE TRANSACTIONS.

               18.1 Assumption or Replacement of Option by Successor. In the
event of (a) a dissolution or liquidation of the Company, (b) a merger or
consolidation in which the Company is not the surviving corporation (other than
a merger or consolidation with a wholly-owned subsidiary, a reincorporation of
the Company in a different jurisdiction, or other transaction in which there is
no substantial change in the stockholders of the Company or their relative stock
holdings and this Option is assumed, converted or replaced by the successor
corporation, which assumption will be binding on the Optionee), (c) a merger in
which the Company is the surviving corporation but after which the stockholders
of the Company immediately prior to such merger (other than any stockholder that
merges, or which owns or controls another corporation that merges, with the
Company in such merger) cease to own their shares or other equity interest in
the Company, (d) the sale of substantially all of the assets of the Company, or
(e) the acquisition, sale, or transfer of more than 50% of the outstanding
shares of the Company by tender offer or similar transaction, this Option may be
assumed, converted or replaced by the successor corporation (if any), which
assumption, conversion or replacement will be binding on the Optionee. In the
alternative, the successor corporation may substitute equivalent options or
provide substantially similar consideration to the Optionee as was provided to
other stockholders. The successor corporation may also issue, in place of
outstanding Shares of the Company held by the Optionee, substantially similar
shares or other property subject to repurchase restrictions no less favorable to
the Optionee. In the event such successor corporation (if any) refuses to assume
or substitute this Option, as provided above, pursuant to a transaction
described in this subsection, this Option will expire on such transaction at
such time and on such conditions as the Committee will determine; provided,
however, that the Committee may, in its sole discretion, provide that the
vesting of this Option will accelerate. If the Committee exercises such
discretion with respect to this Option, this Option will become exercisable in
full prior to the consummation of such event at such time and on such conditions
as the Committee determines, and if this Option is not exercised prior to the
consummation of the corporate transaction, it shall terminate at such time as
determined by the Committee.

               18.2 Other Treatment of Option. Subject to any greater rights
granted to the Optionee under the foregoing provisions of this section, in the
event of the occurrence of any transaction described in Section 18.1, this
Option will be treated as provided in the applicable agreement or plan of
merger, consolidation, dissolution, liquidation, or sale of assets.

        19. AMENDMENT OR TERMINATION OF THE AGREEMENT. The Board may at any time
terminate or amend this Agreement in any respect; provided, however, that the
Board will


                                      -7-


<PAGE>   7
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement


not, without the approval of the Optionee, amend this Agreement in any manner
that requires Optionee's approval.

        20. DEFINITIONS. As used in this Agreement, the following terms will
have the following meanings:

               "BOARD" means the Board of Directors of the Company.

               "CAUSE" means the commission of an act of theft, embezzlement,
fraud, dishonesty or a breach of fiduciary duty to the Company or a Parent or
Subsidiary of the Company.

               "COMMITTEE" means the Compensation Committee of the Board

               "DISABILITY" means a disability, whether temporary or permanent,
partial or total, within the meaning of Section 22(e)(3) of the Internal Revenue
Code of 1986, as amended, as determined by the Committee.

               "FAIR MARKET VALUE" means, as of any date, the value of a share
of the Company's Common Stock determined as follows:

        (a)     if such Common Stock is then quoted on the Nasdaq National
                Market, its closing price on the Nasdaq National Market on the
                date of determination as reported in The Wall Street Journal;

        (b)     if such Common Stock is publicly traded and is then listed on a
                national securities exchange, its closing price on the date of
                determination on the principal national securities exchange on
                which the Common Stock is listed or admitted to trading as
                reported in The Wall Street Journal;

        (c)     if such Common Stock is publicly traded but is not quoted on the
                Nasdaq National Market nor listed or admitted to trading on a
                national securities exchange, the average of the closing bid and
                asked prices on the date of determination as reported in The
                Wall Street Journal; or

        (d)     if none of the foregoing is applicable, by the Committee in good
                faith.

               "PARENT" means any corporation (other than the Company) in an
unbroken chain of corporations ending with the Company if each of such
corporations other than the Company owns stock possessing 50% or more of the
total combined voting power of all classes of stock in one of the other
corporations in such chain.

               "SUBSIDIARY" means any corporation (other than the Company) in an
unbroken chain of corporations beginning with the Company if each of the
corporations other


                                      -8-


<PAGE>   8
                                                        Broadbase Software, Inc.
                                                 Non-Plan Stock Option Agreement

than the last corporation in the unbroken chain owns stock possessing 50% or
more of the total combined voting power of all classes of stock in one of the
other corporations in such chain.

               "TERMINATION" or "TERMINATED" means, for purposes of this
Agreement with respect to the Optionee, that the Optionee has for any reason
ceased to provide services as an employee, officer, director, consultant,
independent contractor, or advisor to the Company or a Parent or Subsidiary of
the Company. An employee will not be deemed to have ceased to provide services
in the case of (i) sick leave, (ii) military leave, or (iii) any other leave of
absence approved by the Committee, provided, that such leave is for a period of
not more than 90 days, unless reemployment upon the expiration of such leave is
guaranteed by contract or statute or unless provided otherwise pursuant to
formal policy adopted from time to time by the Company and issued and
promulgated to employees in writing. In the case of the Optionee is on an
approved leave of absence, the Committee may make such provisions respecting
suspension of vesting of this Option while on leave from the employ of the
Company or a Subsidiary as it may deem appropriate, except that in no event may
this Option be exercised after the expiration of the term set forth in this
Agreement. The Committee will have sole discretion to determine whether the
Optionee has ceased to provide services and the effective date on which the
Optionee ceased to provide services (the "TERMINATION DATE").

        IN WITNESS WHEREOF, the Company has caused this Agreement to be executed
in duplicate by its duly authorized representative and Optionee has executed
this Agreement in duplicate as of the Date of Grant.


BROADBASE SOFTWARE, INC.              OPTIONEE


By: /s/ CHUCK BAY                    /s/ RUSTY THOMAS
   -------------------------------   -------------------------------
                                     (Signature)

Chuck Bay                            Rusty Thomas
----------------------------------   -------------------------------
(Please print name)                   (Please print name)

President
----------------------------------
(Please print title)



                                      -9-


<PAGE>   9
                                    EXHIBIT A


                         STOCK OPTION EXERCISE AGREEMENT


<PAGE>   10
                                    EXHIBIT A

                            BROADBASE SOFTWARE, INC.
                    NON-PLAN STOCK OPTION EXERCISE AGREEMENT

        I hereby elect to purchase the number of shares of Common Stock of
BROADBASE SOFTWARE, INC. (the "Company") as set forth below:

<TABLE>
<S>                                          <C>
Optionee                                     Number of Shares Purchased:
        ----------------------------------                              -----------------------------
Social Security Number:                      Purchase Price per Share:
                       -------------------                            -------------------------------
Address:                                     Aggregate Purchase Price:
        ----------------------------------                            -------------------------------
                                             Date of Option Agreement:
        ----------------------------------                            -------------------------------

Type of Option:  Nonqualified Stock Option   Exact Name of Title to Shares:
               ---------------------------                                 --------------------------
</TABLE>

1.      DELIVERY OF PURCHASE PRICE. Optionee hereby delivers to the Company the
Aggregate Purchase Price, to the extent permitted in the Option Agreement (the
"Option Agreement") as follows (check as applicable and complete):

[ ]     in cash (by check) in the amount of $_____________________, receipt of
        which is acknowledged by the Company;

[ ]     through a "same-day-sale" commitment, delivered herewith, from Optionee
        and the NASD Dealer named therein, in the amount of
        $_______________________________; or

[ ]     through a "margin" commitment, delivered herewith from Optionee and the
        NASD Dealer named therein, in the amount of
        $_________________________________________.

2.      MARKET STANDOFF AGREEMENT. Optionee, if requested by the Company and an
underwriter of Common Stock (or other securities) of the Company, agrees not to
sell or otherwise transfer or dispose of any Common Stock (or other securities)
of the Company held by Optionee during the period requested by the managing
underwriter following the effective date of a registration statement of the
Company filed under the Securities Act, provided that all officers and directors
of the Company are required to enter into similar agreements. Such agreement
shall be in writing in a form satisfactory to the Company and such underwriter.
The Company may impose stop-transfer instructions with respect to the shares (or
other securities) subject to the foregoing restriction until the end of such
period.

3.      TAX CONSEQUENCES. OPTIONEE UNDERSTANDS THAT OPTIONEE MAY SUFFER ADVERSE
TAX CONSEQUENCES AS A RESULT OF OPTIONEE'S PURCHASE OR DISPOSITION OF THE
SHARES. OPTIONEE REPRESENTS THAT OPTIONEE HAS CONSULTED WITH ANY TAX
CONSULTANT(S) OPTIONEE DEEMS ADVISABLE IN CONNECTION WITH THE PURCHASE OR
DISPOSITION OF THE SHARES AND THAT OPTIONEE IS NOT RELYING ON THE COMPANY FOR
ANY TAX ADVICE.

4.      ENTIRE AGREEMENT. The Option Agreement is incorporated herein by
reference. This Exercise Agreement and the Option Agreement constitute the
entire agreement and understanding of the parties and supersede in their
entirety all prior understandings and agreements of the Company and Optionee
with respect to the subject matter hereof, and are governed by California law
except for that body of law pertaining to choice of law or conflict of law.


Date:
-------------------------------              -------------------------------
                                             SIGNATURE OF OPTIONEE


<PAGE>   11
                                 SPOUSAL CONSENT


        I acknowledge that I have read the foregoing Stock Option Exercise
Agreement (the "Agreement") and that I know its contents. I hereby consent to
and approve all the provisions of the Agreement, and agree that the shares of
the Common Stock of Broadbase Software, Inc. purchased thereunder (the "Shares")
and any interest I may have in such Shares are subject to all the provisions of
the Agreement. I will take no action at any time to hinder operation of the
Agreement on these Shares or any interest I may have in or to them.


                                             Date:
                                                  ------------------------------

-----------------------------------
SIGNATURE OF OPTIONEE'S SPOUSE

-----------------------------------
SPOUSE'S NAME - TYPED OR PRINTED

-----------------------------------
OPTIONEE'S NAME - TYPED OR PRINTED