Scammon was appointed brigadier general of volunteers in October 1862, and fought in the major actions of the Kanawha Division. He often clashed with his subordinate, Rutherford B. Hayes. Scammon, by then a division commander, was captured by partisan guerrillas from the 16th Virginia Cavalry on February 3, 1864, when they raided a steamboat carrying General Scammon on the Kanawha River. He returned to duty in South Carolina after being exchanged. He was again captured along the South Carolina coast, but exchanged and when he returned to duty, was placed in command of a brigade in the Department of Florida. He was honorably mustered out in August 1865.