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Eaton served in the Union Army during the American Civil War, enlisting in the 27th Ohio before creation of the 9th Louisiana to which he was by Special Order No. 97 assigned November 6, 1863. On November 13, 1863, by General Order No. 13, Maj. Gen. Ulysses S. Grant appointed him as the Superintendent of Negro Affairs for the Department of the Tennessee ; the army's Department of Freedmen was born of this order, and hundreds of African American fugitives would be employed by the government agency. Essential to Eaton's program, which included religious instruction, reading and writing instruction, and agricultural experiments were two regiments of men determined not to be fit for regular service but for garrison duty. These two were affectionately referred to by Eaton as The Home Guard, also known as The Invalid Corps--the 63rd and 64th regiments, formerly the 9th and 7th Louisiana (respectively). Eaton had served as chaplain of the 27th and continued in this capacity up until his appointment to the 63rd, where he served with several others from the 27th including then 2nd Lt. (later Captain) Thomas A. Walker, Lt. Col. Samuel Thomas, and 1st Lt. George Young.