Fitz-John Porter Court-Martial: 1862-63

General Pope met with Fitz-John Porter on September 2. Porter explained the situation that had confronted him, and Pope told him that he fully accepted the explanation and had no intention of taking any proceedings against his subordinate. However, Pope's reputation was tarnished by the defeat, and McClellan became commander of all troops in the Washington area. On September 17 the bloodiest battle of the war was fought at Antietam, with 12,500 casualties on the Union side and 11,000 Confederate soldiers killed or wounded. General McClellan forced the Confederate army to retreat, but enraged President Lincoln by not pursuing it into Virginia. Shortly before Antietam, General Pope had had a meeting with President Lincoln which, as he subsequently testified, had "opened my eyes to many matters which I had before been loth to believe.…" In November Fitz-John Porter was relieved of his command and ordered court-martialled, although the charges were not brought by General Pope, but by Brigadier General B. S. Roberts, the inspector-general of Pope's Army of Virginia. In November General McClellan's military career also came to an end when President Lincoln replaced him with General Ambrose Burnside.

There were two charges against Fitz-John Porter. The first was that of a violation of the Ninth Article of War, by disobedience of orders. There were five specifications. The first related to Porter's not marching at 1 A.M. as ordered, but deciding to delay his start until 3 A.M. The others related to his failure to attack the rear and flank of Jackson's troops. The second charge was a violation of the Fifty-second Article of War, misbehavior before the enemy, the misbehavior being his retreat following the attack by General Longstreet. There were four specifications, although the last was immediately withdrawn.