STOCK PURCHASE AGREEMENT

Exhibit 10.1

SYNTROLEUM CORPORATION

STOCK PURCHASE AGREEMENT

March 17, 2005

TABLE OF CONTENTS

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STOCK PURCHASE AGREEMENT

This Agreement is entered into effective as of March 17, 2005 by and among Syntroleum Corporation, a Delaware corporation (the “Company”), and Legg Mason Opportunity Trust, a series of Legg Mason Investment Trust, Inc., a Maryland corporation (the “Purchaser”).

SECTION 1.

AUTHORIZATION AND SALE OF COMMON STOCK

1.1 Authorization . The Company has authorized the sale and issuance at the Closing (as hereinafter defined) of a number of shares (the “Shares”) of its common stock, par value $.01 per share (“Common Stock”), determined in accordance with Section 1.2.

1.2 Sale of the Shares . Subject to the terms and conditions hereof, the Purchaser will buy from the Company, and the Company will issue and sell to the Purchaser, 7,000,000 shares of Common Stock for a purchase price per share of $10; provided, however, that if the Closing Market Price (as defined below) is less than $10 per share, then (a) the purchase price per Share shall be the Closing Market Price and (b) the number of Shares to be bought and sold shall, as determined by the Company (in its sole discretion), either remain 7,000,000 shares of Common Stock or be reduced to a number of shares of Common Stock determined by the Company (in its sole discretion), provided that the product of such number of shares multiplied by the Closing Market Price is not less than $25,000,000; and provided, further, that if the Closing Market Price is less than $10 per share, the Company shall have the right to terminate this Agreement and if so terminated, all further obligations of the parties hereunder shall terminate, except that the obligations in Section 7.2 and Sections 8.1 through 8.14 shall survive.

SECTION 2.

CLOSING DATE; DELIVERY

2.1 Closing . The closing of the purchase and sale of the Shares hereunder shall be held at Syntroleum Corporation, 4322 South 49th West Avenue, Tulsa, Oklahoma 74107, on the first Business Day following the Trade Date (as defined below) (the “Closing”), or at such other time and place upon which the Company and the Purchaser mutually agree upon orally or in writing (the date of the Closing is hereinafter referred to as the “Closing Date”).

2.2 Delivery . At the Closing, the Company will deliver to the Purchaser a certificate or certificates, registered in the Purchaser’s name, representing the Shares, against payment of the purchase price therefor, by wire transfer to the Company in accordance with its instructions.

SECTION 3.

REPRESENTATIONS AND WARRANTIES OF THE COMPANY

Except as set forth on the disclosure schedule prepared by the Company and delivered to the Purchaser, dated as of the date hereof (the “Disclosure Schedule”), the Company

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represents and warrants to the Purchaser both as of the date hereof and again as of the Closing as follows:

3.1 Organization and Standing; Subsidiaries; Charter and Bylaws . The Company and each of its Subsidiaries (as hereinafter defined) is a corporation, partnership or limited liability company duly organized, existing and in good standing under the laws of the jurisdiction of its incorporation or organization. The Company and each of its Subsidiaries has all requisite corporate, partnership or limited liability company power and authority to own and operate their respective properties and assets, and to carry on their business as presently conducted. The Company and each of its Subsidiaries currently is qualified to do business in each jurisdiction where the failure to be so qualified has not had and would not reasonably be expected to have, individually or in the aggregate, a material adverse effect on the assets, liabilities, financial condition, operating results or business of the Company and its Subsidiaries, taken as a whole (a “Material Adverse Effect”). The Company has made available to the Purchaser a true, correct and complete copy of the Company’s Certificate of Incorporation, as in full force and effect on the date hereof (the “Charter”), and a true, correct and complete copy of the Company’s Bylaws as in full force and effect on the date hereof (the “Bylaws”).

3.2 Capitalization . The authorized capital stock of the Company consists of 155,000,000 shares, 150,000,000 shares of which are designated as Common Stock, 250,000 shares of which are designated as Series A Junior Participating Preferred Stock, par value $.01 per share (“Series A Junior Preferred Stock”), and 4,750,000 shares of which is undesignated preferred stock, par value $.01 per share (“Undesignated Stock”). As of March 16, 2005, there were 47,240,629 shares of Common Stock outstanding and there were no shares of Series A Junior Preferred Stock or Undesignated Stock outstanding. The outstanding shares of the Company’s capital stock have been duly authorized and validly issued and are fully paid and nonassessable. As of the date hereof, (i) an aggregate of 5,000,000 shares are reserved for issuance under the Company’s 1993 Stock Option and Incentive Plan, and 4,150,849 shares of Common Stock are issuable pursuant to outstanding stock options granted pursuant to the Company’s 1993 Stock Option and Incentive Plan, (ii) an aggregate of 395,370 shares (one percent of the number of shares of Common Stock outstanding on January 1, 2005) are reserved for issuance under the Company’s Stock Option Plan for Outside Directors, and 184,826 shares of Common Stock are issuable pursuant to outstanding stock options granted pursuant to the Company’s Stock Option Plan for Outside Directors, (iii) an aggregate of 1,058,798 shares are reserved for issuance pursuant to stock options granted to Company consultants and officers outside of the Company’s 1993 Stock Option and Incentive Plan, (iv) an aggregate of 1,560,000 shares are reserved for issuance under the SLH Corporation 1997 Stock Incentive Plan, (v) an aggregate of 1,552,000 shares of Common Stock are reserved for issuance pursuant to the Company’s outstanding publicly traded warrants issued on November 4, 2003, (vi) an aggregate of 887,400 shares of Common Stock are reserved for issuance pursuant to the Company’s outstanding publicly traded warrants issued on May 26, 2004, (vii) an aggregate of 1,036,250 shares of Common Stock are reserved for issuance pursuant to outstanding warrants issued to Company consultants and (viii) an aggregate of 11,000 shares of Common Stock are issuable pursuant to outstanding stock options granted to Company employees pursuant to the Company’s 2005 Stock Incentive Plan, which will be submitted for stockholder approval at the Company’s 2005 annual meeting of stockholders. Each outstanding share of Common Stock carries a stock purchase right, which rights entitle the holder to buy one one-hundredth of a share of junior

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preferred stock at a price of $20.8333 per one one-hundredth of a share pursuant to the provisions of the Company’s Second Amended and Restated Rights Agreement dated as of October 24, 2004. Except as described in this Agreement or in the Disclosure Schedule, there are no other options, warrants, conversion privileges or other contractual rights presently outstanding to purchase or otherwise acquire any authorized but unissued shares of the Company’s capital stock or other securities.

3.3 Authorization . The Company has all requisite corporate power and authority to execute and deliver this Agreement, to sell and issue the Shares hereunder and to carry out and perform its obligations under the terms of this Agreement. All corporate action on the part of the Company, its directors and its stockholders necessary for the authorization, execution, delivery and performance of this Agreement by the Company, the authorization, sale, issuance and delivery of the Shares and the performance of all of the Company’s obligations hereunder has been taken or will have been taken prior to the Closing. This Agreement constitutes the valid and binding obligation of the Company, enforceable in accordance with its terms, except as such enforcement is subject to the effect of (i) any applicable bankruptcy, insolvency, reorganization or other laws relating to or affecting creditors’ rights generally, and (ii) general principles of equity (regardless of whether such enforceability is considered in a proceeding in equity or at law). Upon issuance in accordance with the provisions of this Agreement, the Shares will be validly issued, fully paid and nonassessable. The issuance and sale of the Shares contemplated hereby will not give rise to any preemptive rights or rights of first refusal on behalf of any person.

3.4 SEC Reports . The Company has previously made available to the Purchaser true and complete copies of its (i) Annual Report on Form 10-K for its fiscal year ended December 31, 2004, (ii) Current Reports on Form 8-K filed on January 5, 2005, January 19, 2005, January 28, 2005, February 1, 2005, February 17, 2005 and March 8, 2005 and (iii) any other reports or registration statements filed by the Company with the Commission since January 1, 2005, except for preliminary material, which are all the documents that the Company was required to file since that date (collectively, the “SEC Reports”). As of their respective dates, the SEC Reports complied as to form in all material respects with the requirements of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and the rules and regulations of the Commission thereunder applicable to such SEC Reports. As of their respective dates, the SEC Reports, when read together with previously filed SEC Reports, did not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements contained therein, in light of the circumstances under which they were made, not misleading, except as updated, corrected or superseded by subsequently filed SEC Reports. Except as may be indicated therein or in the notes thereto, the audited consolidated financial statements and unaudited interim financial statements of the Company included in the SEC Reports comply as to form in all material respects with applicable accounting requirements and with the published rules and regulations of the Commission with respect thereto, have been prepared in accordance with generally accepted accounting principles applied on a consistent basis throughout the periods covered thereby and fairly present in all material respects the financial condition of the Company as of the dates indicated and the results of operations, changes in stockholders’ equity and cash flows of the Company for the period indicated. Since December 31, 2004, there has been no change in the assets, liabilities, financial condition, operating results or business of the Company and its Subsidiaries, taken as a whole, from that

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reflected in the audited consolidated financial statements and unaudited interim financial statements of the Company included in the SEC reports, except as set forth in the Disclosure Schedule or changes in the ordinary course of business that have not had and would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

3.5 No Conflicts . The execution, delivery and performance of this Agreement, including the issuance of the Shares, have not resulted and will not (i) result in any violation of or conflict with, or constitute a default under, the Company’s Charter or Bylaws, (ii) result in any violation of or conflict with, or constitute a material default under, any mortgage, indebtedness, lease, indenture, contract, agreement, license, instrument, judgment, order, decree, statute, law, ordinance, rule or regulation to which the Company or any of its Subsidiaries is party or otherwise subject to (subject to any required notices or filings with the NNM (as hereinafter defined) and such consents, approvals, authorizations, orders, registrations or qualifications as may be required under state securities or Blue Sky laws in connection with the issuance by the Company of the Shares and the purchase of the Shares by the Purchaser in the manner contemplated herein and in the Final Prospectus and as have not had and would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect), or (iii) result in the creation of any mortgage, pledge, lien, encumbrance or charge upon any of the properties or assets of the Company or any of its Subsidiaries, except in the case of clauses (ii) or (iii) as has not had and would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

3.6 Approvals . The Securities and Exchange Commission (the “Commission”) has issued an order under the Securities Act of 1933, as amended (the “Securities Act”), declaring the Registration Statement effective, and no other consent, approval, authorization, order, registration or qualification of or with any Governmental Authority (as hereinafter defined) is required for the offer and sale of the Shares to the Purchaser, or the consummation by the Company of the transactions contemplated by this Agreement and the Final Prospectus (as hereinafter defined), except such consents, approvals, authorizations, orders, registrations or qualifications as may be required under state securities or Blue Sky laws in connection with the issuance by the Company of the Shares and the purchase of the Shares by the Purchaser in the manner contemplated herein and in the Final Prospectus and as have not had and would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

3.7 Offering . To the best of the Company’s knowledge, the Commission has not issued any order preventing or suspending the use of the Base Prospectus (as hereinafter defined).

3.8 Litigation . There is no action, suit, proceeding or investigation pending or, to the Company’s knowledge, currently threatened against the Company or any Subsidiary of the Company that questions the validity of this Agreement or the right of the Company to enter into such agreement, or to consummate the transactions contemplated hereby, or that would reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect or that would reasonably be expected to materially adversely affect the Company’s ability to consummate the transaction contemplated hereby.

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3.9 Brokers or Finders . The Company has not incurred, and will not incur, directly or indirectly, as a result of any action taken by the Company, any liability for brokerage or finders’ fees or agents’ commissions or any similar charge in connection with this Agreement.

3.10 Limitation on Representations . The Company shall not be deemed to have made any representation or warranty to any Purchaser other than as expressly made by the Company in this Section 3. Without limiting the generality of the foregoing, except as expressly made by the Company in this Section 3, the Company makes no representation or warranty to the Purchaser with respect to (a) any projections, estimates or budgets heretofore delivered or made available to the Purchaser of future revenues, expenses or expenditures or future results of operations or (b) any other information or documents (financial or otherwise) made available to the Purchaser or its counsel, accountants or advisors.

SECTION 4.

REPRESENTATIONS AND WARRANTIES OF THE PURCHASER

The Purchaser represents and warrants to the Company both as of the date hereof and again as of the Closing as follows:

4.1 Investment . The Purchaser is acquiring the Shares in the ordinary course of its business and not with the view to, or for resale in connection with, any distribution thereof. The Purchaser has not offered or sold any portion of the Shares to be acquired by it and has no present intention of reselling or otherwise disposing of any portion of such Shares either currently or after the passage of a fixed or determinable period of time or upon the occurrence or nonoccurrence of any predetermined event or circumstance. The Purchaser shall not resell the Shares in a manner that results in a requirement to deliver a prospectus under Section 5 of the Securities Act. The Purchaser understands that no federal or state agency has passed upon the Shares or made any finding or determination as to the fairness of the investment or any recommendation or endorsement of the Shares. In acquiring the Shares, the Purchaser is acting on its own behalf and is not acting together with any other person or entity for the purpose of acquiring, holding, voting or disposing of the Shares within the meaning of Section 13(d) of the Exchange Act.

4.2 Authorization . The Purchaser has all requisite power and authority to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement. All corporate action on the part of the Purchaser, the Purchaser’s directors and stockholders necessary for the