He resigned from the U.S. Army to take command of a brigade in the Confederate army. He led his men into action at the Battle of First Manassas on the extreme left of the line in a position to prevent a flank attack. His initiative won him the rank of brigadier general. After participating in the Maryland campaign, he was sent west with General Joseph Johnston. He was involved in the Vicksburg campaign before he begin to have problems. He was tried with disobedience and removed from command.