Everything proceeded perfectly, at first. Intelligence derived from one soldier, John Cook, who had been spying for Brown in and around Harpers Ferry for the previous 18 months, provided specific targets. Each soldier had an assignment. Some guarded the Potomac and Shenandoah bridges. Others captured the federal armory and arsenal. A contingent seized the Shenandoah Rifle Works.

Brown's plans began to unravel quickly when a watchman escaped and alerted an incoming train. The train halted, and Heyward Shepherd, a free Black baggage porter, was mortally wounded by Brown’s men—the first casualty of the raid.

Dr. John Starry, awakened by the gunshots, confirmed Shepherd’s shooting and rushed to raise the alarm. His warning quickly mobilized local militias, who arrived via railroad, surrounding Brown by noon. Brown was trapped in the armory’s fire engine house, cut off and outnumbered.