Following the death of its commander, Colonel Patrick Robert Guiney took command of the regiment on 4 August 1862. At this point the Ninth took its place in the newly formed Army of Virginia under the command of General John Pope. The regiment participated in the Second Battle of Bull Run, which resulted in a decisive defeat for the Northern Army. News of the defeat at Bull Run so shook the inhabitants of Washington DC that plans were made to abandon the city before the arrival of the Confederate Army. At his urging, General George Brinton McClellan was given command of the Army of the Potomac and led the army to Antietam Creek near Sharpsburg, Maryland on 17 September 1862 where they successfully engaged General Robert E. Lee’s army.