War began in 1861 Harper chose to follow the Confederate cause. Still a major general in Virginia's state militia, he was given command of the 5th Virginia Infantry Regiment on April 10. Eight days later a force of 2,400 men led by Harper and Brig. Gen. William H. Harman seized the U.S. Army arsenal located at Harpers Ferry in modern-day West Virginia. Despite the fires set by the Union Army forces as they withdrew, Harper's militia managed to salvage 4,000 of the approximately 15,000 muskets in storage there, as well as 300 of the arsenal's milling machines and metal working lathes, plus about 57,000 tools and wooden stocks (all items used in rifle production), which were sent to the Tredegar Iron Works in Richmond, Virginia. On April 28 Confederate Col. Thomas J. "Stonewall" Jackson arrived to assume command of the forces at Harpers Ferry and began to organize the militia into regiments. On May 1, 1861, Harper was appointed a brigadier general in the Virginia Provisional Army, an organization soon added to the overall Confederate States Army. Seven days later he was commissioned a colonel and given command of the 5th Virginia Infantry, one of the regiments that made up the Stonewall Brigade. Harper and the 5th Virginia fought well during the First Battle of Bull Run on July 21, "where his soldierly ability attracted the notice of the army commander." However, Harper resigned from the Confederate Army on September 11, because Jackson refused to allow Harper permission to return home where his wife lay dying. Upon returning to the Shenandoah Valley, Augusta County voters again elected Harper to the Virginia House of Delegates, where he served until 1864. On June 2 of that year, after abolitionist Union General David Hunter's raid into the Shenandoah Valley, Harper accepted re-appointment as a colonel in the Confederate Army in order to form a regiment from reservist companies located in the Shenandoah Valley. During the Valley Campaigns of 1864 under General Jubal Early, Confederate raiders destroyed Harper's original hometown, Chambersburg, Pennsylvania on July 30, 1864 in retaliation for Hunter's campaign as well as its failure to pay ransom. However, Union forces continued to attack the Shenandoah valley. Col. Harper and his troops (under General Early) were routed at the Battle of Piedmont on June 5–6, 1864 and then the Battle of Waynesboro, Virginia on March 2, 1865. Postbellum After the conflict, Harper returned