During the fighting on Maryland Heights, the other Confederate columns arrived and were astonished to see that critical positions to the west and south of town were not defended.

After processing more than 12,000 Union prisoners, Jackson's men then rushed to Sharpsburg, Maryland, to rejoin Lee for the Battle of Antietam.

At the time the garrison at Harpers Ferry – officially the Railroad Brigade of the Middle Department, Eighth Army Corps,[7] the purpose of which was to protect the strategically vital Baltimore and Ohio Railroad and Chesapeake and Ohio Canal, where they passed through the area, and the lower Shenandoah Valley[8]—was the last remaining sizable Union force south of the Potomac River,[7] consisting of about 10,400 men, later joined by 2,500 from the Union garrison at Martinsburg[9]—plus a large cache of small arms as well as artillery pieces, wagons, and Union uniforms.

"[10] As Gen. Robert E. Lee's Army of Northern Virginia (ANV) advanced into Maryland, Lee expected that the Union garrisons that potentially blocked his supply line in the Shenandoah Valley, at Winchester, Martinsburg, and Harpers Ferry, would be cut off and abandoned without firing a shot,[11] but the garrisons, Harpers Ferry specifically, were still manned.

While the rest of the ANV remained at Boonsboro—later minus the corps of Maj. Gen. James Longstreet which Lee sent north to Hagerstown to protect against the reported movement of Pennsylvania militia there,[12] which proved illusory—Lee sent three columns of troops to converge and attack Harpers Ferry from separate directions.

He left 3,000 men near Brownsville Gap to protect his rear and moved 3,000 others toward the Potomac River to seal off any eastern escape route from Harpers Ferry.

Walker's men were ordered to destroy the aqueduct carrying the Chesapeake and Ohio Canal across the Monocacy River where it empties into the Potomac, but his engineers had difficulty demolishing the stone structure and the attempt was eventually abandoned.

White led Walker on a meandering route around the Short Hill Mountain to reach the base of Loudoun Heights four days later on September 13.

[17] So the attack on Harpers Ferry that had been planned for September 11 was delayed, increasing the risk that McClellan might engage and destroy a portion of Lee's army while it was divided.

Miles divided his 10,400 garrison troops into four brigades, making sure that the raw, inexperienced men he had recently received were balanced by more experienced soldiers.

[18][19] On nearby Camp Hill, he placed a 1,000-man brigade of heavy artillery and supporting infantry to cover the position on Bolivar Heights.

Some of these men, including those of the 126th New York, had been in the Army only 21 days and lacked basic combat skills; they had only just arrived at Harpers Ferry.

[24] On September 12 they encountered the approaching men from Kershaw's South Carolina brigade, who had been moving slowly through the very difficult terrain on Elk Ridge.

Their commander, Col. Ford, felt ill that morning and stayed back two miles (3 km) behind the lines, leaving the fighting to Col. Eliakim Sherrill, the second-ranking officer.

Sherrill was wounded by a minié ball through the cheek and tongue while rallying his men and had to be carried from the field, making the green troops grow panicky.

Ford later insisted he had the authority from Miles to order the withdrawal, but a court of inquiry concluded that he had "abandoned his position without sufficient cause," and recommended his dismissal from the Army.

Charles Russell of the 1st Maryland Cavalry with nine troopers to slip through the enemy lines and take a message to McClellan, or any other general he could find, informing them that the besieged town could hold out only for 48 hours.

Unbeknownst to Miles, only a single Confederate regiment now occupied the crest, after McLaws had withdrawn the remainder to meet the Union assault at Crampton's Gap.

Davis and Col. Arno Voss led their 1,400 cavalrymen out of Harpers Ferry on a pontoon bridge across the Potomac, turning left onto a narrow road that wound to the west around the base of Maryland Heights in the north toward Sharpsburg.

Despite a number of close calls with returning Confederates from South Mountain, the cavalry column encountered a wagon train approaching from Hagerstown with James Longstreet's reserve supply of ammunition.

They were able to trick the wagoneers into following them in another direction and they repulsed the Confederate cavalry escort in the rear of the column, and the southern teamsters found themselves surrounded by Federals in the morning.

Capturing more than 40 enemy ordnance wagons, Davis had lost not a single man in combat, the first great cavalry exploit of the war for the Army of the Potomac.

So disgusted were the men of the garrison with Miles's behavior, which some claimed involved being drunk again, it was difficult to find a man who would take him to the hospital.

[40] Confederate soldiers feasted on Union food supplies and helped themselves to fresh blue Federal uniforms, which would cause some confusion in the coming days.

Hill at Harpers Ferry to manage the parole of Federal prisoners and began marching to join the Battle of Antietam.

[43] The War Department appointed a special commission under Major General David Hunter to determine the reasons for the loss at Harpers Ferry.

During 15 days of testimony, resulting in over 900 pages of evidence, the commission focused on Miles' competence and loyalty, his defense of the garrison, the action of his subordinate officers, and missed opportunities for escape and rescue.

[44][45] Finally, although Colonel Miles was dead, and the commission expressed some reluctance to criticize an officer who could not speak on his own behalf, he was nevertheless described as having "incapacity, amounting to almost imbecility [for] the shameful surrender of this important post."

"[44] General Henry Halleck—who, as General-in-Chief had refused McClellan's request to attach the Harpers Ferry garrison to the Army of the Potomac, thus denying him an additional 11,000 troops, and leaving Miles in an untenable situation—was not mentioned in the commission's criticism.