During the Chickamauga campaign, Mitchell served as George H. Thomas's Chief of Cavalry for the Army of the Cumberland. Just before the Third Battle of Chattanooga, he was ordered to Washington, D.C., for court-martial duty. According to some sources, this was due to severe wounds which incapacitated him from field duty but this is contradicted in the "Official Records" by Mitchell's own correspondence. Whether incapacitated or not, he would not see active campaigning again, and for the remainder of the Civil War, he commanded the District of Nebraska, then the District of North Kansas, and finally the District of Kansas. He saw service in Colorado Territory in January 1865, following the Indian raid on Julesburg, Colorado, on the Overland Trail, but he did not succeed in locating the Indian camp on the Republican River until after they had departed.