Pvt. Cooper was listed as being present on roll calls through May '64. On June 11th he was captured by the enemies near Louisa Courthouse, Va. He was sent to Fortress Monroe, Va. June 20th and on July 25, 1864 he was transferred to Elmira Prison, N.Y.

As many of the prisoners at Elmira, Pvt. John R. Cooper died. The cause was chronic diarrhoea. He was buried at Elmira September 2, 1864 in grave # 139.