Lieutenant Jones immediately made secret preparations. He had trains of powder laid through the buildings, and when the force of thirteen hundred Virginians had approached to within a mile of the arsenal, at nine o'clock on the evening of April 17, the torch was applied, and the flames ran through the works, which were quickly burning. Some of the powder trains had been wet by the Southern sympathizers among the workmen, but the result was a practical destruction of nearly all that would have been valuable as munitions of war. The powder that was stored in the buildings exploded from time to time, effectually preventing serious efforts to put out the fire. The garrison was withdrawn { 28} across the Potomac and marched back to Carlisle. When the Virginians came up the next morning, they found only the burning arsenal buildings to greet them.
Enough property was rescued from the destruction to make the capture a useful one to the Confederates, however; and the possession of Harper's Ferry gave them command of an important line of communication with Washington, by the Baltimore and Ohio Railroad. Anticipating the use of this line for the transportation of Western troops to Washington, Gen. Kenton Harper, commanding the Virginians, stopped the first train through; but his only capture was the person of Gen. William S. Harney, of the regular army, who was on his way to Washington to resign his commission rather than engage in the civil war. He was made a prisoner and sent to Richmond, whence he was allowed to proceed on his errand. General Harney did not resign, but was presently sent to Missouri to command the Department of the West. But his conciliating method of dealing with the enemy, together with his uncertain loyalty, caused him to be relieved very soon. The strategic value of Harper's Ferry was developed under Col. Thomas J. Jackson (afterward the celebrated "Stonewall"), who was made colonel commandant of all the Virginia forces, superseding all the previously existing militia generals. Robert E. Lee had been given the general command of the State troops, with Jackson as his executive officer, and by a legislative ordinance every militia officer above the grade of captain had been relegated to private life unless reappointed by the governor under the new dispensation.