Two days after the Battle of Antietam, Palmer was captured while scouting at the personal direction of McClellan, seeking information on any preparations by Lee's army to cross the Potomac River back into Virginia. He was on the Confederate side of the river, again garbed in civilian clothes and accompanied by a local blacksmith and a parson as his guides, attempting to recross to the Union side after midnight when he was captured by Confederate artillerymen sent to guard the dam he used for the crossing. When questioned, Palmer gave his name as "W.J. Peters," and claimed to be an engineer on an inspection trip. He was interrogated by General William N. Pendleton, who thought he was a spy. He was detained and sent to Richmond, Virginia, with a rambling note from Pendleton that was ignored.