Scott was appointed colonel of the 12th Louisiana Infantry Regiment on August 13, 1861. He served at the Battle of Belmont, although not actively engaged, and at the battles of Island Number Ten, New Madrid, Fort Pillow, the Siege of Vicksburg, including the Battle of Baker's Creek and the operations of General Joseph E. Johnston in Mississippi in which he tried to relieve the forces besieged at Vicksburg, and during the Atlanta Campaign, initially under the command of Lieutenant General Leonidas Polk.