Lee's repulse of McClellan's army in late June and early July considerably changed the tenor of the war in the east. Through the spring McClellan had rolled his mighty army irrepressibly toward Richmond. This, combined with the defeat of Johnston's army at Shiloh in April, made the outlook for an overall Union victory look good, even imminent. But by early July, it was clear that McClellan's army was not much of a threat to Richmond. Indeed, it was unfit for offensive action any time soon.

Lee felt so anyway, and he began to look north, where a new threat was forming. This was an army under the command of John Pope, growing stronger in the vicinity of Fredericksburg. Pope's army was made up of parts of McDowell's army and elements of the Federal armies that had been fighting against Stonewall Jackson in the Shenandoah Valley. Pope called his force the Army of Virginia. The idea was that he would move south to press the Confederate Army of Northern Virginia between it and McClellan's Army of the Potomac. Meanwhile, Lincoln had placed General Halleck in charge of all Union armies and brought him to Washington from his pervious command in the west. It was hoped this new arrangement would help coordinate moves between the various Union forces, especially between Pope's army and McClellan's.

However, in 1862, the Union was not quite up to the task. Halleck visited McClellan on the James River but could not get him moving to again threaten Lee. Lee sensed this and knew it gave him an opportunity. He must deal with Pope before McClellan stirred again. With this in mind, Lee sent Stonewall Jackson and 25,000 men north toward Pope's army. In short order, Halleck, seeing that McClellan would not move against Richmond, ordered McClellan to return the Army of the Potomac to northern Virginia in order to reinforce Pope. This, of course, would take some time.

Lee again took a large gamble, dividing his army a second time and sending Jackson west toward the Shenandoah Valley. Jackson disappeared behind the Bull Run Mountains just shy of the valley, then swung north and east again, marching to the rear of Pope's army. Jackson seized the huge concentration of Union army supplies at Manassas Junction, burning what his men could not eat or carry. Pope set off in pursuit, but Jackson was nowhere in sight, having hidden along a wooded ridge near the battlefield where First Manassas had been fought the previous July. As Pope attempted to find Jackson's force, Jackson pounced on one of Pope's divisions, setting up the battle of Second Manassas.