He was initially commissioned as a major general in the Virginia militia on May 4, but the Virginia Convention decided two weeks later that only one major general was required in the state army and Robert E. Lee was their choice. Johnston was then offered a state commission as a brigadier general, which he declined, accepting instead a commission as a brigadier general in the Confederate States Army on May 14. Johnston relieved Colonel Thomas J. "Stonewall" Jackson of command at Harpers Ferry in May and organized the Army of the Shenandoah in July.