When the militia stormed the rifle works, the three men inside dashed for the shallow Shenandoah, hoping to wade across. Two of them—John Kagi, vice president of Brown's provisional government, and Lewis Leary, an African-American—were shot dead in the water. The black Oberlin student, John Copeland, reached a rock in the middle of the river, where he threw down his gun and surrendered. Twenty-year-old William Leeman slipped out of the engine house, hoping to make contact with the three men Brown had left as backup in Maryland. Leeman plunged into the Potomac and swam for his life. Trapped on an islet, he was shot dead as he tried to surrender. Throughout the afternoon, bystanders took potshots at his body.
Through loopholes—small openings through which guns could be fired—that they had drilled in the engine house's thick doors, Brown's men tried to pick off their attackers, without much success. One of their shots, however, killed the town's mayor, Fontaine Beckham, enraging the local citizenry. "The anger at that moment was uncontrollable," says Frye. "A tornado of rage swept over them." A vengeful mob pushed its way into the Galt House, where William Thompson was being held prisoner. They dragged him onto the railroad trestle, shot him in the head as he begged for his life and tossed him over the railing into the Potomac.
By nightfall, conditions inside the engine house had grown desperate. Brown's men had not eaten for more than 24 hours. Only four remained unwounded. The bloody corpses of slain raiders, including Brown's 20-year-old son, Oliver, lay at their feet. They knew there was no hope of escape. Eleven white hostages and two or three of their slaves were pressed against the back wall, utterly terrified. Two pumpers and hose carts were pushed against the doors, to brace against an assault expected at any moment. Yet if Brown felt defeated, he didn't show it. As his son Watson writhed in agony, Brown told him to die "as becomes a man."
Soon perhaps a thousand men—many uniformed and disciplined, others drunk and brandishing weapons from shotguns to old muskets—would fill the narrow lanes of Harpers Ferry, surrounding Brown's tiny band. President James Buchanan had dispatched a company of Marines from Washington, under the command of one of the Army's most promising officers: Lt. Col. Robert E. Lee. Himself a slave owner, Lee had only disdain for abolitionists, who "he believed were exacerbating tensions by agitating among slaves and angering masters," says Elizabeth Brown Pryor, author of Reading the Man: A Portrait of Robert E. Lee Through His Private Letters. "He held that although slavery was regrettable, it was an institution sanctioned by God and as such would disappear only when God ordained it." Dressed in civilian clothes, Lee reached Harpers Ferry around midnight. He gathered the 90 Marines behind a nearby warehouse and worked out a plan of attack. In the predawn darkness, Lee's aide, a flamboyant young cavalry lieutenant, boldly approached the engine house, carrying a white flag. He was met at the door by Brown, who asked that he and his men be allowed to retreat across the river to Maryland, where they would free their hostages. The soldier promised only that the raiders would be protected from the mob and put on trial. "Well, lieutenant, I see we can't agree," replied Brown. The lieutenant stepped aside, and with his hand gave a prearranged signal to attack. Brown could have shot him dead—"just as easily as I could kill a musquito," he recalled later. Had he done so, the course of the Civil War might have been different. The lieutenant was J.E.B. Stuart, who would go on to serve brilliantly as Lee's cavalry commander.
Lee first sent several men crawling below the loopholes, to smash the door with sledgehammers. When that failed, a larger party charged the weakened door, using a ladder as a battering ram, punching through on their second try. Lt. Israel Green squirmed through the hole to find himself beneath one of the pumpers. According to Frye, as Green emerged into the darkened room, one of the hostages pointed at Brown. The abolitionist turned just as Green lunged forward with his saber, striking Brown in the gut with what should have been a death blow. Brown fell, stunned but astonishingly unharmed: the sword had struck a buckle and bent itself double. With the sword's hilt, Green then hammered Brown's skull until he passed out. Although severely injured, Brown would survive. "History may be a matter of a quarter of an inch," says Frye. "If the blade had struck a quarter inch to the left or right, up or down, Brown would have been a corpse, and there would have been no story for him to tell, and there would have been no martyr."
Meanwhile, the Marines poured through the breach. Brown's men were overwhelmed. One Marine impaled Indianan Jeremiah Anderson against a wall. Another bayoneted young Dauphin Thompson, where he lay under a fire engine. It was over in less than three minutes. Of the 19 men who strode into Harpers Ferry less than 36 hours before, five were now prisoners; ten had been killed or fatally injured. Four townspeople had also died; more than a dozen militiamen were wounded.
Only two of Brown's men escaped the siege. Amid the commotion, Osborne Anderson and Albert Hazlett slipped out the back of the armory, climbed a wall and scuttled behind the embankment of the Baltimore and Ohio Railroad to the bank of the Potomac, where they found a boat and paddled to the Maryland shore. Hazlett and another of the men whom Brown had left behind to guard supplies were later captured in Pennsylvania and extradited to Virginia. Of the total, five members of the raiding party would eventually make their way to safety in the North or Canada.
Brown and his captured men were charged with treason, first-degree murder and "conspiring with Negroes to produce insurrection." All of the charges carried the death penalty. The trial, held in Charles Town, Virginia, began on October 26; the verdict was guilty, and Brown was sentenced on November 2. Brown met his death stoically on the morning of December 2, 1859. He was led out of the Charles Town jail, where he had been held since his capture, and seated on a small wagon carrying a white pine coffin. He handed a note to one of his guards: "I John Brown am now quite certain that the crimes of this guilty land: will never be purged away; but with blood." Escorted by six companies of infantry, he was transported to a scaffold where, at 11:15, a sack was placed over his head and a rope fitted around his neck. Brown told his guard, "Don't keep me waiting longer than necessary. Be quick." These were his last words. Among the witnesses to his death were Robert E. Lee and two other men whose lives would be irrevocably changed by the events at Harpers Ferry. One was a Presbyterian professor from the Virginia Military Institute, Thomas J. Jackson, who would earn the nickname "Stonewall" less than two years later at the Battle of Bull Run. The other was a young actor with seductive eyes and curly hair, already a fanatical believer in Southern nationalism: John Wilkes Booth. The remaining convicted raiders would be hanged, one by one.
Brown's death stirred blood in the North and the South for opposing reasons. "We shall be a thousand times more Anti-Slavery than we ever dared to think of being before," proclaimed the Newburyport (Massachusetts) Herald. "Some eighteen hundred years ago Christ was crucified," Henry David Thoreau opined in a speech in Concord on the day of Brown's execution, "This morning, perchance, Captain Brown was hung. These are the two ends of a chain which is not without its links. He is not Old Brown any longer; he is an angel of light." In 1861, Yankee soldiers would march to battle singing: "John Brown's body lies a-mouldering in the grave, but his soul goes marching on."
On the other side of the Mason-Dixon line, "this was the South's Pearl Harbor, its ground zero," says Frye. "There was a heightened sense of paranoia, a fear of more abolitionist attacks—that more Browns were coming any day, at any moment. The South's greatest fear was slave insurrection. They all knew that if you held four million people in bondage, you're vulnerable to attack." Militias sprang up across the South. In town after town, units organized, armed and drilled. When war broke out in 1861, they would provide the Confederacy with tens of thousands of well-trained soldiers. "In effect, 18 months before Fort Sumter, the South was already declaring war against the North," says Frye. "Brown gave them the unifying momentum they needed, a common cause based on preserving the chains of slavery."