General Robert E. Lee took command of the Confederate Army of Northern Virginia in the middle of the Battle of Seven Pines after the wounding of General Johnston and what appeared to be a nervous breakdown of Major General Gustavus Smith. The battle caused McClellan to pause and regroup, giving Lee three weeks to familiarize himself with his new command before launching the Seven Days Battles on June 25.
The Army of the Valley District under Major General Thomas Jackson fought the Battles of Cross Keys on June 8 and Port Republic on June 9, defeating the last Union pursuers in the Shenandoah Valley. From June 18 – 25 Jackson moved his command from the Shenandoah to reinforce Lee at Richmond. After this point the command was operationally Jackson’s Command of the Army of Northern Virginia.