The city of Winchester, Virginia, and the surrounding area, were the site of numerous battles during the American Civil War, as contending armies strove to control the lower Shenandoah Valley. Winchester changed hands more often than any other Confederate city.
Background
John Brown's raid on Harpers Ferry
Ties between Winchester and the American Civil War are considered to have begun with the suppression of John Brown's raid in October 1859, in nearby Harpers Ferry. Colonel Lewis Tilghman Moore, of the 31st Virginia Militia of Frederick County, assembled 150 militiamen from the Marion Guards, the Morgan Continentals, and the Mount Vernon Riflemen, and moved them on the Winchester and Potomac Railroad to Harpers Ferry, to the east. Ironically, the first death of Brown's raid was Heyward Shepherd, a free black from Winchester who worked for the B&O Railroad; he was buried in Winchester's colored cemetery with military honors. Following the raid, Judge Richard Parker of Winchester presided over the trial of John Brown, sentencing the insurrectionist to hang.
The bodies of a son of John Brown and three other raiders, one white (Jeremiah Anderson) and two Blacks (John Anthony Copeland and Shields Green), were taken to the Winchester Medical College for use in medical education. During the two months of the first Union occupation (March 12–May 25, 1862), the Union forces would certainly have learned of this. The bodies of the three dissected bodies were long vanished when Union forces arrived two years later; the only remains were unlabeled bones, taken out in the country and tossed haphazardly into a pit.
In contrast, the body of Watson Brown had not been dissected but had been turned into a medical specimen. Half the skull and the brain had been removed, but the muscles and blood vessels had been preserved and stained. When Union troops arrived his body was on display in the one-room museum of the college, with a label that read: "John Brown's son—thus always with Abolitionists", and the lips "purposely distorted in disrespect". It has been skinned, with the skin made into moccasins and the scraps given out as souvenirs. The troops were also surely informed of the Black community's fear of and hatred for the college, because it regularly robbed Black graves.
John Brown was the Union's hero and the Confederacy's villain in the Civil War. He died to end slavery. Union soldiers marched to John Brown's Body, which became the Battle Hymn of the Republic. It was the assassination of Lincoln that displaced Brown from the nation's consciousness. To dishonor a son of Brown, who also died fighting slavery, and displaying the body as a crude lesson to abolitionists, was deeply offensive to the Union officers.
The Union officers set the college's building on fire on May 16, 1862. They did not allow fire engines to extinguish the blaze, and the building burned to the ground. The college never reopened.
Secession deliberations
Neither Winchester nor the Commonwealth of Virginia were particularly fond of secession from the Union. Virginia was not a cotton state, and the Valley's economy and culture centered around small family-owned farms producing wheat and cattle. However pro-Union sentiment was often conditional. Historian William A. Link writes:
At the same time, the resolutions renounced secession, promised "unfaltering attachment" to the Union, proposed boycotting imports from some Northern states, and called for, if necessary, a national convention to resolve the sectional issues.