Stone was appointed Colonel of the 14th U.S. Infantry Regiment on May 14, and then a brigadier general in the Union Army that August, to rank from May 17. He commanded a brigade in Maj. Gen. Robert Patterson's Army of the Shenandoah during the First Bull Run campaign in June and July. Stone then was given command of a division, called the Corps of Observation, guarding the fords along the upper Potomac River that fall.