After the first battle of Manassas the First Brigade was known as the "Stonewall Brigade."

From July to November, 1861, Jackson spent the greater part of every day drilling the men under him and in trying to convert them into well-disciplined, obedient troops. During the first week in November he was sent from Manassas to command the Shenandoah Valley district and this meant parting from the soldiers whom he had reason to admire and who in turn held him in highest esteem. A short time later they were destined to reunite under circumstances which would try the courage of the brigade and commander. To the delight of all, the Stonewall Brigade was assigned to Winchester soon after Jackson established his headquarters there and for the next few months rigid training was given them again.

About the middle of March 1862, Jackson abandoned Winchester. This was after some of the Union concentration near Manassas and Centreville was broken up and General Banks made no move to offer battle, so the Confederates withdrew without a fight and occupied Strasburg eighteen or twenty miles southward. The evacuation of Winchester was made reluctantly, for good roads in each direction connected the city with outlying districts, fertile farms nearby could furnish the invading army with rations and Banks could receive from or send troops to West Virginia or the army south of Washington. Feeling that Jackson's small force was not of any special danger, Shields' corps was sent in pursuit of the Confederates and most of Banks' troops were ordered to another field. Jackson continued up the Valley and stopped at Mount Jackson, hoping the Federals would follow.

The Confederate general learned from Ashby, his cavalry commander, that the enemy was retreating. It was Lee's intention that the Union corps in the Valley be retained there so that assistance could not be offered McClellan, the Northern general who was maneuvering in the eastern part of Virginia with the ultimate aim of striking Richmond. McClellan hoped to attack the capital of the Confederacy by combining his army with that of McDowell, whom he could call to the area of war when necessary. So it was to be Jackson's duty to keep them in the Valley and perhaps to withdraw some of the Northern troops from near Richmond.

On March 22nd Ashby with his troopers and a few guns engaged Shields in a skirmish just south of Winchester. He believed there was only a small force of Federals present, so well had Shields hidden his men, and he reported to Jackson that the troops were small in number. The next day Jackson sent reinforcements to Ashby and then followed later with his whole force in the direction of Kernstown which is south of Winchester and but a short distance off. There the battle of Kernstown began and continued until dark. Jackson's troops were defeated and retreated southward. As a result of this encounter Shields was reinforced and the strong Union force remained in the Valley.

The Federal generals were apparently satisfied with the victory and in spite of urgings from the Secretary of War, Stanton, to pursue Jackson they remained inactive for nearly a month.

Banks assumed the offensive on April 17th, and surprised Ashby, taking one of his companies prisoner. The Virginians burned the railroad station at Mount Jackson and fell back while the Union cavalry established themselves at New Market.

The Confederate General Ewell had a force of 8,000 men on the Upper Rappahannock which is some distance east of the mountains. This corps was left at its location in order to rush to the defense of Fredericksburg or Richmond or across the mountains to the Valley. Jackson knew that he must not allow Banks to control the mountain pass, thus severing communication between the two Confederate forces. He determined upon a forced march for his men and on the eighteenth they reached Harrisonburg. He continued over to Swift Run Gap and encamped near there.

Banks followed his cavalry to New Market, crossed over to Luray and seized the bridges, driving back a detachment of Jackson's men sent there to defend them. Later he sent two of his five brigades to Harrisonburg and the rest stayed at New Market.

Jackson's next move was to McDowell, a town about twenty-seven miles northwest of Harrisonburg. The march was made in the most circuitous manner: from Swift Run Gap to Port Republic, to Brown's Gap which is about twelve miles southeast of their camp at Elk Run Valley, to Staunton and then west to McDowell. This strategy was used so that he might deceive Banks, Fremont and Milroy, the Federal commanders in and near the Valley, into thinking for a while that he was leaving the Valley to join forces at Richmond. Jackson proposed to strike each Union force located in this section of Virginia but he believed an encounter with Milroy commanding the weakest corps should be made before attacking Banks. The Battle of McDowell occurred on May 8th, and was a victory for Jackson. He followed the enemy in their retreat as far as Franklin. A squadron of Ashby's cavalry spent much time in blocking any of the passes which Fremont might use in crossing the mountains to reinforce Banks. Bridges were burned and rocks and trees were placed across the roadways. Jackson's object was thus thoroughly achieved: