Following the Confederate victory at the Battle of Bull Run in late July, Baxter gradually abandoned his campaign against secession, and began to reconcile with the new Confederate government. In September 1861, he took the Oath of Allegiance to the Confederacy, in part to provide legal assistance to Unionists who had been arrested, and in part because he felt the North could not defeat the South in a war. While many secessionists, such as Landon Carter Haynes, welcomed Baxter's defection, others, such as "Knoxville Register" editor J. Austin Sperry, doubted his sincerity. In September 1861, Baxter ran for the district's seat in the Confederate Congress, but was badly defeated by William G. Swan.