Joseph Eggleston Johnston was another talented Confederate officer who had recurrent problems with Jefferson Davis. However, he was a very effective, well-liked leader who held important commands in the eastern and western theaters throughout the war and did his very best against long odds.

Johnston was born in Virginia in 1807. He attended West Point and saw quite a bit of combat following graduation, including service in the Seminole War and the Mexican War. In the 1850s, he saw duty in the Kansas Territory during the bloody conflict there and was made quartermaster general of the U.S. Army in June 1860. He resigned his commission in April 1861, when Virginia seceded from the Union.

Johnston was made a brigadier general in the Confederate army in May 1861 and was the commander of the Confederate troops that won the First Battle of Manassas, though he deferred the planning of strategy to Beauregard, who had a greater knowledge of the battlefield. It was the first military victory for the Confederate army and a stunning and unexpected blow against the overly confident Union.

The following month Johnston was named a full general and appointed to command the Department of the Potomac. He was wounded in the Battle of Seven Pines in May 1862 and temporarily relieved of duty while he recuperated. In November, Johnston was appointed commander of the Department of the West, but Jefferson Davis refused to support his battle strategy, and Johnston suffered humiliating defeats. As a result of these losses, Johnston's reputation among Confederate leaders in Richmond suffered greatly. Eventually, Johnston was brought back east to command the Army of Tennessee and ordered to stop Sherman's march toward Atlanta in 1864.