After convalescing from his injuries and serving in the Bureau of Conscription he resigned his commission on June 16, 1863, and requested a transfer to the Trans-Mississippi Dept.
There he served on John Bankhead Magruder's staff and was then given the command of a Texas brigade of infantry.
Gen. Kirby Smith recommended his promotion to brigadier-general on March 16, 1865, although there is no confirmation of his appointment.
He was given a presidential pardon, dated August 15, 1865, sponsored by the Attorney General and the Hon.
He then returned to West Virginia, and lived in Wheeling with his wife Ella Clemens' family.