In 1861, Scott resigned from the State Senate to enter the Union army. He was appointed lieutenant-colonel of the 3rd Iowa Regiment. There are few records of Scott's service during the Civil War, with the exception of his leadership during the Battle of Liberty, in Missouri. In September 1861, he led a force of about 600 men from Cameron, on the 15th, towards Liberty. He left his camp in Centreville, at 2:00 am on the 17th. He arrived in Liberty, sent scouts out to find the enemy, and, about 11:00 am, skirmishing began. At noon, Scott marched in the direction of the firing, approached Blue Mills Landing and, at 3:00 am, struck the Confederate pickets. The Union forces were forced to fall back, so the battle ended in a Confederate victory. In 1862 he was promoted to colonel of the Thirty-second Infantry where he served with distinction until May 1864.
