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General Joseph E. Johnston had been in command of the Confederate Army of the Shenandoah for about three weeks, since May 24, 1861, and he did not like the position he was in at Harper's Ferry. The town was important for both sides, but it was impossible to defend; it would change hands eight times during the war. On Saturday, June 15, 1861, Johnston withdrew his army, some 10,000 men organized into four brigades, toward Winchester.
Harper's Ferry, Virginia (now West Virginia) had a very strategic location on the Baltimore & Ohio Railroad. It was where the Potomac and Shenandoah Rivers and the states of Maryland and Virginia met. It was also the site of the United States Armory and Arsenal, one of only two such facilities in the country (the other at Springfield, Illinois) where small arms were produced for the U.S. Army. Until April 1861, that is.
When Virginia seceded, the U.S. Army garrison at the arsenal evacuated. They tried to burn the buildings and destroy the equipment before they left, but local citizens saved the machinery. Major General Kenton Harper of the Virginia Militia quickly organized two thousand militiamen at Harper's Ferry and put Brigadier General Thomas Jackson in charge. The equipment was sent to Richmond for safe keeping, and this group of militia formed the nucleus of Johnston's army.
Johnston had taken command in May when Virginia Governor John Letcher turned the state troops over to Confederate control. Jackson became one of Johnston's most important lieutenants.
Robert E. Lee, who had overall command of the state troops until they were turned over to the Confederacy, had advised Johnston to hold onto Harper's Ferry. To give it up, he said, "would be depressing to the cause of the South." But Johnston was in an impossible position. The town sat on a low flood plain with the heights of the Blue Ridge Mountains all around it. It was at the bottom of a bowl. On top of that, two Federal armies had his attention -- Robert Patterson's army (also named the Army of the Shenandoah) was just across the Potomac in Maryland and George McClellan's was somewhere to his west in the Virginia mountains. Johnston had to find a more favorable position. He eventually settled at Bunker Hill.
During his time at Harper's Ferry, Jackson had commandeered the B & O trains that came through, 42 locomotives and 386 freight cars. Most of these were wrecked and thrown into the river, but Jackson used horses to haul fourteen locomotives and some boxcars by road to Strasburg, where they were put on the Manassas Gap Railroad for Confederate use.
An aside: Rather quickly after the start of the war, the pro-Unionist counties of western Virginia would break away from the rest of the state, seceding from the secessionists to form the new state of West Virginia. Harper's Ferry, then in Virginia would be located in the new state. In 1890, the United States Board on Geographic Names, which is responsible for formally naming municipalities and natural landmarks, removed most apostrophes so as to not imply ownership of a place. What was once Harper's Ferry, Virginia, is now Harpers Ferry, West Virginia.
Another aside: Harper's Ferry was the site of John Brown's raid in October 1859.