Nathan J. Johnson was 39 years old when he joined the 93rd New York Infantry on 3 November 1861. He joined at Granville, New York, but his residence was not listed. He was commissioned on 11 December 1861, as a captain and assigned to 'I' Company in the 93rd New York.
On 13 April 1864, he was discharged from the 93rd for promotion, and, on 15 April 1864, he was commissioned into the 115th New York Infantry as its lieutenant colonel. He is listed as wounded 18 August 1864 at Deep Bottom Run, Virginia; on 1 October 1864 at Chaffin's Farm, Virginia; and for a third time on 15 January 1865, at Fort Fisher, North Carolina. He later received a bevet promotion to colonel and was actually promoted to that rank on 17 June 1865, with a promotion date as of 29 April 1865. He mustered out with the regiment on 17 June 1865 at Raleigh, North Carolina and led it home to New York.
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