Document:

EX-10.51

EXHIBIT 10.51

THIRD AMENDMENT TO THE MEZZANINE WARRANT AGREEMENT

THIS THIRD AMENDMENT TO THE MEZZANINE WARRANT AGREEMENT (the “Amendment”) is made effective as
of March 8, 2005, between Alion Science and Technology Corporation, a Delaware corporation (the
“Company”), and Illinois Institute of Technology, an Illinois not-for-profit corporation (“IIT”).

WHEREAS, the Company, IIT Research Institute, an Illinois not-for-profit corporation
affiliated with and controlled by IIT (“IITRI”), and Alion Science and Technology Corporation
Employee Ownership, Savings and Investment Trust (the “Trust”) entered into that certain Mezzanine
Warrant Agreement dated as of the 20th day of December 2002 (the “Mezzanine Warrant
Agreement”), pursuant to which the Company issued to IITRI warrants to purchase Five Hundred
Twenty-Four Thousand Two Hundred Twenty-Eight and Nine-Tenths (524,228.9) shares of the Company’s
$0.01 par value per share common stock (“Common Stock”), of which warrants to purchase Five Hundred
Four Thousand Nine Hundred One and Nine-Tenths (504,901.9) shares of Common Stock remain
outstanding as of the date of this Amendment;

WHEREAS, as of July 1, 2004, IITRI transferred to IIT all its rights and interests in the
Mezzanine Warrant Agreement;

WHEREAS, the Company and IIT entered into that certain First Amendment to the Mezzanine
Warrant Agreement effective as of December 16, 2004 (the “First Amendment”), pursuant to which the
parties agreed to certain amendments to the Mezzanine Warrant Agreement;

WHEREAS, the Company and IIT entered into that certain Second Amendment to the Mezzanine
Warrant Agreement effective as of January 24, 2005 (the “Second Amendment”), pursuant to which the
parties agreed to certain further amendments to the Mezzanine Warrant Agreement (as amended by the
First Amendment and the Second Amendment, the “Amended Mezzanine Warrant Agreement”);

WHEREAS, the Company and IIT desire to amend Sections 3(l)(i) and 16(c) of the Amended
Mezzanine Warrant Agreement as set forth herein; and

WHEREAS, the Trust is a party to the Amended Mezzanine Warrant Agreement only for the purposes
of Sections 6, 7, 15 and 17 through 25 of the Amended Mezzanine Warrant Agreement, and
pursuant to Section 18 of the Amended Mezzanine Warrant Agreement, Sections 3(l)(i) and 16(c) may
be amended by the mutual written agreement of the Company and IIT, without the need to obtain the
Trust’s consent.

NOW, THEREFORE, in consideration of the premises set forth above and the respective covenants
and agreements contained in this Amendment, and for other good and valuable consideration, the
receipt and sufficiency of which is hereby mutually acknowledged, and intending to be legally
bound, the parties hereto hereby agree as follows:

1. Amendments to the Amended Mezzanine Warrant Agreement.

(a) Section 3(l)(i) of the Amended Mezzanine Warrant Agreement is hereby amended by deleting
the entire text of Section 3(l)(i) and substituting in lieu thereof:

“SARs issued to employees, consultants, officers or directors of the Company or any
of its Subsidiaries with an exercise price no less than Fair Value, except for such
amount of SARs that, at the time of issuance, would cause the aggregate number of
SARs then outstanding (excluding any SARs that have (x) been exercised, (y) expired,
terminated unexercised, or become unexercisable or (z) been forfeited or otherwise
terminated, surrendered or canceled) to be in excess of:

(1) two percent (2%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the first anniversary of the Effective Date;

(2) four percent (4%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the second anniversary of the Effective Date;

(3) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
six percent (6%) of the number of then outstanding shares of Common Stock on a fully
diluted basis (assuming the exercise of all outstanding options, warrants and rights
and the conversion into Common Stock of all convertible securities), at the third
anniversary of the Effective Date;

(4) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
eight percent (8%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fourth anniversary of the Effective Date; and

(5) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
ten percent (10%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fifth anniversary of the Effective Date.”

(b) Section 16(c) of the Amended Mezzanine Warrant Agreement is hereby amended by deleting the
entire text of Section 16(c) and substituting in lieu thereof:

“As long as none of the clauses (a), (b) or (c) of the definition of Current
Market Price in Section 3(c)(ii) is applicable to the Common Stock, all SARs
issued by the Company will be issued with an exercise price no less than the per
share value of the Common Stock as set forth in the then most recent appraisal
performed by an independent appraiser at the Company’s request in connection with
the ESOP. If one of the clauses (a), (b) or (c) of the definition of Current Market
Price in Section 3(c)(ii) is applicable to the Common Stock, all SARs issued
by the Company will be issued with an exercise price no less than the then current
Current Market Price. All SARs issued by the Company will vest in accordance with
the terms of the Company’s Stock Appreciation Rights Plan, as in effect at the time
of issuance. The Company will not issue SARs that cause the aggregate number of
outstanding SARs (excluding any SARs that have been exercised, that have expired,
terminated unexercised, or become unexercisable or that have been forfeited or
otherwise terminated, surrendered or cancelled), at the time of issuance, to be in
excess of:

(1) two percent (2%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the first anniversary of the Effective Date;

(2) four percent (4%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the second anniversary of the Effective Date;

(3) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
six percent (6%) of the number of then outstanding shares of Common Stock on a fully
diluted basis (assuming the exercise of all outstanding options, warrants and rights
and the conversion into Common Stock of all convertible securities), at the third
anniversary of the Effective Date;

(4) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
eight percent (8%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fourth anniversary of the Effective Date; and

(5) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
ten percent (10%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fifth anniversary of the Effective Date.”

2. Waivers. The parties hereto hereby agree that neither the execution of this
Amendment nor any provision contained herein shall be deemed to in any way affect or act to
restrict or terminate the provisions of Section 2 of the First Amendment or Section 2 of the
Second Amendment, including without limitation, any waivers and releases granted to and/or given
for the benefit of the Company therein.

3. Remainder of the Amended Mezzanine Warrant Agreement Not Affected. Except as
set forth in Section 1 hereof, the terms and provisions of the Amended Mezzanine Warrant Agreement
remain in full force and effect without change, amendment, waiver or modification.

4. Ratification. As modified hereby, the Amended Mezzanine Warrant Agreement and its
terms and provisions are hereby ratified for all purposes and in all respects.

5. Counterparts. This Amendment may be executed in one or more counterparts, all of
which taken together shall constitute one instrument.

6. References. From and after the date provided above, all references to the Amended
Mezzanine Warrant Agreement shall be deemed to be references to the Amended Mezzanine Warrant
Agreement as modified hereby.

7. Governing Law. This Amendment shall be governed by and construed in accordance
with the laws of the State of Delaware, without regard to the conflict of laws principles thereof.

8. Conflict. In the event of any conflict between the terms of this Amendment and the
Amended Mezzanine Warrant Agreement, the terms of this Amendment shall govern.

[Signatures follow on next page]

1

IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed by its
officers thereunto duly authorized as of the date hereof.

	 	 	 
	Alion Science and Technology Corporation	 	Illinois Institute of Technology
	By: /s/ Bahman Atefi

	 	By: /s/ Lewis Collens
	 

	 	 
	Name: Bahman Atefi

Title: Chief Executive Officer

	 	Name: Lewis Collens

Title: President
	 
	 	 

2EX-10.52

EXHIBIT 10.52

THIRD AMENDMENT TO THE ALION MEZZANINE WARRANT AGREEMENT

THIS THIRD AMENDMENT TO THE ALION MEZZANINE WARRANT AGREEMENT (the “Amendment”) is made
effective as of March 8, 2005, between Alion Science and Technology Corporation, a Delaware
corporation (the “Company”), and Bahman Atefi, an individual (“Holder”).

WHEREAS, the Company, Holder, and Alion Science and Technology Corporation Employee Ownership,
Savings and Investment Trust (the “Trust”) entered into that certain Alion Mezzanine Warrant
Agreement dated as of the 20th day of December 2002 (the “Alion Mezzanine Warrant
Agreement”), pursuant to which the Company issued to Holder warrants to purchase Twenty-Two
Thousand Sixty-One and Seven-Tenths (22,061.7) shares of the Company’s $0.01 par value per share
common stock (“Common Stock”);

WHEREAS, the Company and Holder entered into that certain First Amendment to the Alion
Mezzanine Warrant Agreement effective as of December 15, 2004 (the “First Amendment”), pursuant to
which the parties agreed to certain amendments to the Alion Mezzanine Warrant Agreement;

WHEREAS, the Company and Holder entered into that certain Second Amendment to the Alion
Mezzanine Warrant Agreement effective as of January 24, 2005 (the “Second Amendment”), pursuant to
which the parties agreed to certain further amendments to the Alion Mezzanine Warrant Agreement (as
amended by the First Amendment and the Second Amendment, the “Amended Alion Mezzanine Warrant
Agreement”);

WHEREAS, the Company and Holder desire to amend Sections 3(l)(i) and 16(a) of the Amended
Alion Mezzanine Warrant Agreement as set forth herein; and

WHEREAS, the Trust is a party to the Amended Alion Mezzanine Warrant Agreement only for the
purposes of Sections 6, 7, 15 and 17 through 25 of the Amended Alion Mezzanine Warrant
Agreement, and pursuant to Section 18 of the Amended Alion Mezzanine Warrant Agreement, Sections
3(l)(i) and 16(a) may be amended by the mutual written agreement of the Company and Holder, without
the need to obtain the Trust’s consent.

NOW, THEREFORE, in consideration of the premises set forth above and the respective covenants
and agreements contained in this Amendment, and for other good and valuable consideration, the
receipt and sufficiency of which is hereby mutually acknowledged, and intending to be legally
bound, the parties hereto hereby agree as follows:

1. Amendments to the Amended Alion Mezzanine Warrant Agreement.

(a) Section 3(l)(i) of the Amended Alion Mezzanine Warrant Agreement is hereby amended by
deleting the entire text of Section 3(l)(i) and substituting in lieu thereof:

“SARs issued to employees, consultants, officers or directors of the Company or any
of its Subsidiaries with an exercise price no less than Fair Value, except for such
amount of SARs that, at the time of issuance, would cause the aggregate number of
SARs then outstanding (excluding any SARs that have (x) been exercised, (y) expired,
terminated unexercised, or become unexercisable or (z) been forfeited or otherwise
terminated, surrendered or canceled) to be in excess of:

(1) two percent (2%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the first anniversary of the Effective Date;

(2) four percent (4%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the second anniversary of the Effective Date;

(3) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
six percent (6%) of the number of then outstanding shares of Common Stock on a fully
diluted basis (assuming the exercise of all outstanding options, warrants and rights
and the conversion into Common Stock of all convertible securities), at the third
anniversary of the Effective Date;

(4) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
eight percent (8%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fourth anniversary of the Effective Date; and

(5) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
ten percent (10%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fifth anniversary of the Effective Date.”

(b) Section 16(a) of the Amended Alion Mezzanine Warrant Agreement is hereby amended by
deleting the entire text of Section 16(a) and substituting in lieu thereof:

“As long as none of the clauses (a), (b) or (c) of the definition of Current
Market Price in Section 3(c)(ii) is applicable to the Common Stock, all SARs
issued by the Company will be issued with an exercise price no less than the per
share value of the Common Stock as set forth in the then most recent appraisal
performed by an independent appraiser at the Company’s request in connection with
the ESOP. If one of the clauses (a), (b) or (c) of the definition of Current Market
Price in Section 3(c)(ii) is applicable to the Common Stock, all SARs issued
by the Company will be issued with an exercise price no less than the then current
Current Market Price. All SARs issued by the Company will vest in accordance with
the terms of the Company’s Stock Appreciation Rights Plan, as in effect at the time
of issuance. The Company will not issue SARs that cause the aggregate number of
outstanding SARs (excluding any SARs that have been exercised, that have expired,
terminated unexercised, or become unexercisable or that have been forfeited or
otherwise terminated, surrendered or cancelled), at the time of issuance, to be in
excess of:

(1) two percent (2%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the first anniversary of the Effective Date;

(2) four percent (4%) of the number of then outstanding shares of Common Stock
on a fully diluted basis (assuming the exercise of all outstanding options, warrants
and rights and the conversion into Common Stock of all convertible securities) at
the second anniversary of the Effective Date;

(3) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
six percent (6%) of the number of then outstanding shares of Common Stock on a fully
diluted basis (assuming the exercise of all outstanding options, warrants and rights
and the conversion into Common Stock of all convertible securities), at the third
anniversary of the Effective Date;

(4) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
eight percent (8%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fourth anniversary of the Effective Date; and

(5) the sum of (a) thirty-three thousand (33,000), plus (b) the amount equal to
ten percent (10%) of the number of then outstanding shares of Common Stock on a
fully diluted basis (assuming the exercise of all outstanding options, warrants and
rights and the conversion into Common Stock of all convertible securities), at the
fifth anniversary of the Effective Date.”

2. Waivers. The parties hereto hereby agree that neither the execution of this
Amendment nor any provision contained herein shall be deemed to in any way affect or act to
restrict or terminate the provisions of Section 2 of the First Amendment or Section 2 of the
Second Amendment, including without limitation, any waivers and releases granted to and/or given
for the benefit of the Company therein.

3. Remainder of the Amended Alion Mezzanine Warrant Agreement Not Affected.
Except as set forth in Section 1 hereof, the terms and provisions of the Amended Alion Mezzanine
Warrant Agreement remain in full force and effect without change, amendment, waiver or
modification.

4. Ratification. As modified hereby, the Amended Alion Mezzanine Warrant Agreement
and its terms and provisions are hereby ratified for all purposes and in all respects.

5. Counterparts. This Amendment may be executed in one or more counterparts, all of
which taken together shall constitute one instrument.

6. References. From and after the date provided above, all references to the Amended
Alion Mezzanine Warrant Agreement shall be deemed to be references to the Amended Alion Mezzanine
Warrant Agreement as modified hereby.

7. Governing Law. This Amendment shall be governed by and construed in accordance
with the laws of the State of Delaware, without regard to the conflict of laws principles thereof.

8. Conflict. In the event of any conflict between the terms of this Amendment and the
Amended Alion Mezzanine Warrant Agreement, the terms of this Amendment shall govern.

[Signatures follow on next page]

1

IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed by its
officers thereunto duly authorized as of the date hereof.

	 	 	 	 	 
	Alion Science and Technology Corporation	 	 
	By: /s/ Jack Hughes

	 	 	 	By: /s/ Bahman Atefi
	 
	 	 	 	 
	 
	 	 
	 
	 	 	 	 
	Name:

Title:

	 	Jack Hughes

Senior Vice President and

Chief Financial Officer
	 	Name: Bahman Atefi

Title: Chief Executive Officer

	 
	 	 	 	 

2

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