In late 1862 his regiment was sent to Louisiana, and garrisoned at New Orleans and Baton Rouge. Captain Agnus was wounded on 27 May 1863, during the siege of Port Hudson, he was promoted to major on 2 September, and for a time had command of his regiment. He served in Texas, and, after attaining the rank of lieutenant-colonel, was ordered eastwards to join the 19th Corps. He served under General Philip Sheridan, taking part in the battles of Opequon, Fisher's Hill, Winchester, and Cedar Creek. His last service was in the Department of the South, as inspector general of the Department, where he was commissioned to dismantle old Confederate forts in South Carolina, Georgia, and Florida, and turn all the property over to the U.S. government. He received the brevet of brigadier-general of volunteers on 13 March 1865, making him the youngest brigadier-general in the army at the time. Agnus was mustered out of service on 22 August 1865.