The federal government constructed two arsenal buildings at Harpers Ferry to store the weapons produced at the armory. In 1859 there were 100,000 weapons stored in the arsenal buildings, which played a role in the John Brown raids. Brown intended to use firearms seized at Harpers Ferry to commence a war to end slavery, but failed to do so. Sixteen months later, at the outbreak of the Civil War, only 15,000 weapons were stored at Harpers Ferry. The years between John Brown's raid and the Civil War, the majority of the arms at the United State Arsenal were distributed to Southern states under the instruction of Secretary of War John B. Floyd, a politician who was loyal to Southern interests.
When Virginia seceded from the Union, in 1861, Governor John Letcher ordered the Virginia militia to seize the armory and arsenal at Harpers Ferry. Captain Turner Ashby led the militia towards Harpers Ferry and once they were close they could hear an explosion. The two arsenal buildings were set ablaze by the retreating Union forces, under Lt. Roger Jones command, and 15,000 weapons were destroyed.
Close to 100 years after the Civil War, the National Park Service's archeologists discovered the original foundations of the two arsenal buildings, which buried for generations. They also found thousands of pieces of burned weapons, which included melted and twisted barrels, bayonets, ramrods, and lock plates. Today the arsenal ruins are outlined to attain a better understanding of their role in Harpers Ferry's history.