Under a new militia law in 1864, Harrison was appointed colonel in charge of Georgia's First Military District with the duties of destroying whiskey stills and tracking down deserters. Soon, Harrison's command was required to oppose Sherman's March to the Sea. When they reached the Savannah area, Sherman's men pillaged Harrison's home and property at Montieth. In December 1864, Harrison was taken prisoner while visiting his devastated property. Harrison was released from prison before the end of the war but refused to take the oath of allegiance to the United States government.