Following the victory at Second Bull Run the Federal army was in some disarray in and retreat. It’s commander, John Pope was losing control and his nerves and he did not know what to do. Fearing Lee cutting him off from Washington or catching him while he was reforming Pope ordered a retreat from Centreville to Washington but an order from the general-in-chief in Washington turned him around to attack Robert E. Lee.
Lee had not pursued Pope following the victory because his army was tired from weeks of marching and for some three days of fighting but he was not going to sit idly by and wait for Pope to regroup. Stonewall Jackson was already in motion to try to get behind Pope at Centreville while James Longstreet kept the other wing on the battlefield to deceive Pope. Pope had two options to get to Washington, the Warrenton Turnpike and the Little River Turnpike and both converged at Germantown, Virginia. That was Jackson’s objective but his men were worn down but Pope was unaware of this movement.
That changed overnight with a report of Confederate cavalry at Germantown. Pope dismissed this report but soon received another about a large force of infantry on the march. Now he realized he was in trouble and ordered the army to continue to retreat into Washington. When daylight came on September 1 Pope sent infantry from several different commands to reconnoiter and to block Jackson. The bulk of the blocking force came from IX Corps soldiers under Isaac Stevens and III Corps soldiers under Phil Kearney.