In both the eastern and the western theatres of war, Confederate armies were marching north.
In the west, Gen. E. Kirby Smith’s army had crossed from Tennessee into Kentucky, with the goal of advancing on the Ohio River. In Tennessee, the Confederates under Gen. Braxton Bragg were marching north out of Chattanooga to join Gen. Smith’s command near Frankfort. In the east, Gen. Robert E. Lee’s Army of Northern Virginia had crossed the Potomac River near Leesburg and occupied Frederick, Md. His goal was to carry the war into Pennsylvania.
President Jefferson Davis in Richmond wrote to his commanders, urging Lee, Bragg and Smith to make it clear to the citizens of Kentucky and Maryland that “the Confederate Government is waging this war solely for self-defence, that it has no design of conquest or any other purpose than to secure peace and the abandonment by the United States of its pretensions to govern a people who have never been their subjects and who prefer self-government to a Union with them.”
Near Rockville, Md., outside of Washington, the Union Army of Virginia under Maj. Gen. John Pope was dissolved and his three corps reunited with Maj. Gen. George McClellan’s reorganized Army of the Potomac. Gen. Pope, now a bitter and defeated man, received orders to command the Department of the Northwest; consisting of Wisconsin, Minnesota, Iowa, Nebraska and Dakota territories; his first assignment was to quell the Sioux uprising now in full sway in Minnesota.
In Frederick, Md., Maj. Gen. Thomas “Stonewall” Jackson’s troops occupied the town, and found all the shops and stores closed and the streets deserted. The Confederates treated Frederick courteously, with no looting or pillaging.
Panic and concern spread through the east and west; panic over where generals Bragg and Smith would be leading their men, and what the objectives were of the Army of Northern Virginia. The Union garrisons at Harpers Ferry and Martinsburg, Va. were cut off from Washington, and Union cavalry skirmished with Confederate troops in Maryland nearly every day.
In Cincinnati, the militia was called out to try and stop the Confederates from crossing the Ohio River should Gen. Smith’s troops approach the city from the Kentucky side of the river. In Indiana, Gov. Oliver Perry Morton called upon his citizens to form military companies along the Ohio River should Gen. Smith’s men come that way. In Minnesota, the murderous Sioux Indians besieged a Federal garrison at Birch Coulee.
As the second week of September drew to a close, Confederate troops entered Hagerstown, Md., and then Gen. Jackson marched his command towards Harpers Ferry, not wishing to leave a Federal garrison at his rear. Gen. McClellan’s army began slowly marching from Rockville northwest to oppose the Confederates in western Maryland. Maj. Gen. Nathaniel Banks commanded Washington’s defenses north of the city, and Maj. Gen. Samuel Heintzelman took command of the capital’s defenses south of the Potomac River. On Friday, Sept. 12, in Pennsylvania, the archives, bonds and treasure of the state were moved to New York from Harrisburg and Philadelphia in anticipation of Gen. Lee’s incursion. The mayor of Philadelphia was authorized to defend his city.
Before leaving Frederick on the advance north, Gen. Lee had issued Special Orders No. 191, field orders for the operation of his army. Gen. Jackson was to march on Harpers Ferry while other troops were sent to cover Crampton’s Gap and Turner’s Gap in South Mountain, and Gen. James Longstreet’s command was to go through Boonsborough, Md. to protect the rear of the Army of Northern Virginia. A copy of these orders was to play an important role the following week.