By the fall of 1862 the Armory at Harpers Ferry was destroyed but the area around Harpers Ferry was still of significant strategic value. To secure this area along the flank of Washington D.C. and the strategic B&O Railroad, 1,400 Union troops were stationed at Harpers Ferry and nearby Martinsburg. The once profitable manufacturing center was in ruins. Only 100 remained of the prewar population of over 3,000. One Union soldier commented that "the entire place wasn't worth $10."
Colonel Dixon S. Miles positioned most of his forces in Harpers Ferry and along a strong defense line at Bolivars Heights but failed to strongly defend positions overlooking his forces from Maryland Heights and Loudoun Heights. Because the position was so vulnerable to attack, Lee expected Federal troops to retreat once attacked. At the start of the Battle of Harpers Ferry, approximately 12,500 Federal troops held nearly indefensible positions.
Under the command of "Stonewall" Jackson, Confederate troops attacked lightly defended Union positions on Maryland Heights on September 12. Driving off these forces after a brief skirmish, he quickly positioned Confederate artillery on Maryland and Loudoun Heights. Over 12,000 Union troops were trapped.
By the morning of September 14, Confederate artillery was in position and began a devastating bombardment of Federal positions on Maryland Heights were defended by only one Confederate. Miles took no action other than to endure the bombardment and fight back with limited artillery.
On the morning of September 15, after a brief conference, Union officers agreed to surrender. Over 12,000 Union troops and a large store of supplies and munitions were surrendered to Jackson's troops. Until Bataan, this would remain the largest single surrender of American forces.