Confederate Army of the Shenandoah The Army of the Shenandoah was an army of the Confederate States of America during the American Civil War ; it was organized to defend the Shenandoah Valley of Virginia in the early months of the war . The army was transferred to reinforce the Confederate Army of the Potomac at the First Battle of Bull Run , which was its only major action . After the battle , the army was merged into the Army of the Potomac . History . The Army of the Shenandoah originated with the various militia and volunteer companies sent to seize and defend the town of Harpers Ferry , Virginia ( modern day West Virginia ) . To organize and train the companies , Virginia state commander Robert E . Lee initially appointed Thomas J . Jackson to command the post . Jackson formed five regiment s of infantry and a battery of artillery from the various companies , forming the basis of the Stonewall Brigade . On May 15 , Joseph E . Johnston replaced Jackson as commander of Harpers Ferry and continued to receive additional regiments from throughout the Confederacy . He would eventually have four brigade s of infantry and an independent regiment of cavalry , the 1st Virginia Cavalry commanded by J . E . B . Stuart . In mid - June , forces from the Union Department of Pennsylvania commanded by Robert Patterson began moving south towards Harpers Ferry . Fearing that the terrain around the town made it indefensible , Johnston had the bridges and as much equipment in the town as possible destroyed and retreated south to Winchester ; Patterson remained along the Potomac River rather than pursue Johnston . Over the next few weeks , both forces watched each other , only engaging in battle once at Falling Waters on July 2 . After spending almost two weeks waiting on the Potomac and receiving reinforcements , Patterson started advancing towards Winchester but had moved only before encountering Stuart ' s regiment screening Johnston ' s army . Patterson halted again and consulted his officers , who advised caution ; this advice , along with the refusal of several regiments which were due for mustering out to remain any longer , convinced Patterson to cancel the advance . This allowed Johnston to follow orders he received on July 18 to transfer his army to reinforce P . G . T . Beauregard ' s Army of the Potomac at Manassas Junction . The movement started that evening , with each brigade marching to Piedmont where it boarded a train for Manassas Junction . Since there was only one train on the Manassas Gap Railroad , the brigades arrived one at a time ; the artillery and cavalry marched overland . The final units of Johnston ' s army arrived on the afternoon of July 21 . Since he was senior to Beauregard , Johnston had command over the two armies present . Before Johnston arrived at Manassas , Beauregard had drawn up plans for an attack on the Union army of Irvin McDowell across Bull Run on July 21 , using brigades from both armies , and Johnston approved the plan , allowing Beauregard to issue the necessary orders in his name . However , the orders were vague and contradictory , which confused the brigade commanders and prevented the attack from taking place . On the morning of July 21 , McDowell launched his own attack on the Confederate left wing , defended by one of Beauregard ' s brigades . As the battle escalated in the area of Matthews Hill and Henry House Hill , additional Confederate brigades were moved to the left flank . Eventually , all four of Johnston ' s brigades and four out of Beauregard ' s eight brigades were engaged in this area . It was while defending Henry House Hill that Jackson received his nickname of " Stonewall " , which also became the name of his brigade . After the battle Johnston ' s and Beauregard ' s commands were consolidated into the Department of Northern Virginia , with their merged army using the name " Army of the Potomac " ; Johnston retained command of the army , with Beauregard remaining as second in command until his transfer to the western theater . Order of Battle at Manassas . Army of the Shenandoah : General Joseph E . Johnston