Johnston graduated eighth in the class of 1826 at West Point. After eight years of service, he resigned to care for his terminally ill wife. He returned to service during the Mexican War, but joined the Confederacy in 1861 as the second ranking general in the Confederate Army. He was given command of the western theater of operations. He commanded forces in the Department of Kentucky. He was involved in actions at Mill Springs, Fort Henry, Fort Donelson, Corinth, Pittsburgh Landing, and finally Shiloh. While fighting at Shiloh in late April 1862, he was mortally wounded.