Six minutes later it was all over, and the wounded John Brown and several of his accomplices were dragged out onto the grass. Knocking down the double doors of the engine-house was hot work, but the marines accomplished it, and the local militia swarmed in. One officer met Brown and attacked him with his sword. The sword point broke, but Brown was wounded by a U.S. Marine who stabbed him twice with a bayonet.

Out on the grass, Brown and three or four survivors were interrogated by Colonel Lee, Lieutenant Stuart, and a group of civilian leaders. Time and again, the Virginians asked Brown why he would attempt such a bold, really insane, venture, and each time Brown either scorned to answer or gave a quick reply to the effect that the Almighty had directed him to do so. Lieutenant Stuart took Brown to task, saying that the Bible did not authorize this kind of violence, to which Brown replied that he had his own opinion on that score. The most significant part of the interrogation was when an anonymous person posed the following question:

This was the heart of the matter. To Brown, setting the slaves free seemed like a wonderful thing, the culmination of a lifelong dream and the fulfillment of a biblical necessity. To the people who lived in and around Harpers Ferry, the idea of the slaves being freed was terrifying. They expected it would result in a massacre. By this point, the discussion had become moot, however. Practically no slaves had appeared at Harpers Ferry, and the 1,500 pikes had hardly been used.