Here is my first pass at transcribing Gen. Cooper's application for a pardon to President Andrew Johnson.

I can send jpg images of the pages to anyone who wants to cross-check my spellings and answer the ???? notes I have inserted.

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To His Excellency Andrew Johnson,
President of the United States

The undersigned, your Petitioner, encouraged so to do by the proviso annexed to the enumeration of classes of persons excepted from the amnesty and pardon granted by your Excellency in your proclamation dated May 24th A.D. 1865 --- would respectfully represent --- That he is by birth a Mississippian, and by adoption a citizen of the Chickasaw Nation of Indians --- that he was appointed from the State of Mississippi by President Pierce, Indian Agent for Choctaws on the 8th of April 1853, reappointed and confirmed by the Senate and commissioned for four years 8th Feb 1854; was appointed 8th March 1858 by ??? Buchanan, agent for Choctaws and Chickasaws for four years; that tho’ a Democrat, at the solicitation of the Choctaws and Chickasaws, he consented to serve, if reappointed, as their agent under President Lincoln’s administration, recognizing the legality of his election, and not considering it a sufficient cause for dissolution of the Union. Your Petitioner was among that class of Southern men, who deprecated hostilities between the North and the South, and hoped till the last that a rupture might be averted; but as Southern man, when it had taken place, tho’ having no hand in bringing it about, felt bound to take sides with their section. Your Petitioner continued to discharge the duties of Indian Agent until the 4th of May A.D. 1861 when his office having been surrounded by an armed body of men and important dispatches for Major Emory U.S.A. commanding at Fort Washita taken from him, becoming satisfied that he could no longer serve as an officer of the United States, he resigned and forwarded his resignation to of the office of Indian Agent to Washington City. The whole country was in a blaze of excitement, and the revolution fully inaugurated before the return of your Petitioner from the City of Washington to Indian Country. The country was already in possession of troops from Texas, the protection of the United States forces having been withdrawn. Under these circumstances, the legislature of the Chickasaw Nation met in the latter part of May 1861, and declared that the United States having withdrawn its protection had left them “free and independent” to adopt such measures as their judgment were necessary and proper for self preservation and defense. A law was passed authorizing the Government to raise troops for the defense of the Country, acting as an Independent Nation, foreign to the United States --- they adopted your Petitioner as a Citizen, and gave him the command of their forces. Under this authority your Petitioner proceeded to organize a force for the defense of the Indian Country, and the preservation of order. Soon afterwards to wit: on the 12 of July 1861a Treaty of Alliance was concluded with the so called Confederate States, which bound the Choctaws and Chickasaws to furnish a regiment of mounted men for their service --- and your Petitioner organized and reported on the 18th of August, 1861. He also acted as Indian Agent for the so called Confederate States, tho’ so far as he is informed, no commission was issued to him as such. Your Petitioner served as Colonel under Brig. Gen. Benjamin McCullough’s orders in the year 1861 --- afterwards under Brig. Genls. Pike, Roane, Steele and Maxey, until March 1865, when under orders from Gen. E.K. Smith he was assigned to the command of the District of the Indian Country. Your Petitioner in 1862, was nominated for appointment as a Brigadier, but from some cause it was not acted on by the Senate of the so called Confederate States --- again in May 1863 he was appointed, ad interim, a Brig. General, but is not informed whether he was ever confirmed by the Senate of the so called Confederate States. The only regular commission, except that of Colonel, your Petitioner ever received from the so called Confederate States was that of Superintendent of Indian Affairs dated March 7th 1865, which reached him after the surrender of the Trans-Mississippi Department, and of course was not accepted. From this, however, he infers that his appointment of Brig. Genl was not confirmed by the Senate of the so called Confederate States as the two offices could not legally be held by the same person at one and the same time. Your Petitioner continued to exercise the functions of Brig. General commanding the District of the Indian Territory and Ex. Officio Superintendent of Indian Affairs until the surrender of the Trans-Mississippi Department May 26, 1865 --- but is somewhat at a loss to determine what was his true legal status under the so called Confederate States.

He avers that while acting as Military Officer of the so called Confederate States he endeavored to conduct the war upon civilized principles, and treated prisoners of war in accordance therewith.

So soon as it was ascertained that the South would probably surrender the Trans-Mississippi Department, your Petitioner advised the Indian authorities to call together the Indian Council of the Nations and Tribes in alliance with the so called Confederate States, and take immediate steps to renew treaties, and restore ancient relations of Peace and Friendship with the United States --- and he urged all the influential people to bring about a general pacification of the Indians, restore order, and provide for the indigent and suffering, by obtaining contributions of food and clothing for them from the counties of Texas adjoining the Indian Territory.

As Commanding Officer of the Indian Dept., your Petitioner has been always ready and willing to carry out the terms of surrender agreed upon between Gen. Camby of the U.S.A and Smith of the late C.S. Army.

This was prevented by officers of the United States entering into a Truce, with the Indian Authorities, without communicating or consulting with your Petitioner --- that the fault lay with them, and not with your Petitioner, was admitted by Brig. Gen. Buxlye ???, commanding frontier District at the time your Petitioner applied for Parole which was granted.

Your Petitioner has continued his efforts to reconcile the Indians to the new order of things and to induce them to cheerfully accept and adapt themselves to the present policy of the U.S. Government and he is now willing in good faith to accept the results of the late war, and support the policy of the administration as indicated by your Excellency.

For evidence relative to his character and conduct before the war, during its continuance, and since the surrender your Petitioner respectfully refers to a memorial in his behalf forwarded by the Chickasaw and other Indian Delegations (who lately conclude peace with the United States) thro’ the hands of the Hon. D. N. Cooley, Comm. of Indian Affairs, and also to testimony from Gov. W.L. Sharkey, late Provisional Governor of Mississippi, Governor Isaac Murphy of Arkansas, Gen. Throckmorton of Texas, Hon. D.N. Cooley Comm. of Indian Affairs, Gov. W. Colbert and others of the Chickasaw Nation, ???? Major Gen. H.J. Hunt U.S.A., Commanding Frontier District, and others.

In conclusion your Petitioner desires to call your Excellency’s attention to the fact that he is differently situated from others under the ban of the Government inasmuch as he does not reside within any state or organized territory of the United States. He therefore hopes that he will not be held to a strict compliance with the regulations prescribed for citizens of the states who apply for a special pardon --- but that your Excellency will examine and act upon this his petition in the same liberal spirit which dictated your Excellency’s proclamation of “amnesty and pardon”.

Respectfully submitted,

Douglas H. Cooper