Fleming was the son of Edward Bates, the Attorney General for Abraham Lincoln during the Civil War. When the Lincoln government invaded Missouri in 1861, Bates' son Fleming joined the Confederate Army and resisted the overthrow of the state government. In the spring of 1862 Fleming enlisted in Captain Von Phul's Company of Missouri Light Artillery C.S.A. He was shortly thereafter elected lieutenant of the company. In March of 1863 he was stationed in Little Rock, Arkansas and afterward served under General Sterling Price in the Trans-Mississippi Department. After the war Fleming returned to St. Louis. His forgiving father died with his son by his side.