After the outbreak of the Civil War, Johnson resigned his
United States Army commission and received the rank of
colonel in the 12th Georgia Infantry on July 2, 1861. The 12th Georgia fought in Gen.
Robert E. Lee's first campaign in western Virginia, at the
Battle of Greenbrier River. He was promoted to
brigadier general on December 13, 1861. He was ordered to defend Allegheny mountain, where a route from Cheat Mountain passed southwards then east over the mountain and to Shenandoah valley. His position was strong but still overextended. He was eventually ordered to retreat to a better position on Valley Mountain, but before making the move his forces (six regiments) were struck on their position by a surprise attack of Union forces who were based on Cheat Mountain, some distance northwards. This force was commanded by union general
Robert Milroy, who would become Johnson's nemesis. (This brigade-sized force was given the grandiose name "Army of the Northwest".)
Valley Campaign In the winter of 1861–62, Johnson's army cooperated with
Maj. Gen. Thomas J. "Stonewall" Jackson in the early stages of
Jackson's Valley Campaign. While Jackson marched his army into the mountains of the present-day
Eastern Panhandle of West Virginia to conduct raids on the
Baltimore and Ohio Railroad, Johnson was tasked with protecting against a Union invasion of the "upper," more elevated areas of the Shenandoah Valley near
Staunton, Virginia. His Army of the Northwest constructed a series of breastworks and trenches atop Shenandoah Mountain which they named simply
Fort Edward Johnson. At the
Battle of McDowell, Johnson was severely wounded with a bullet to the ankle, which took a long time to heal. He returned to
Richmond for his convalescence and remained there for nearly a year, active in the social scene. Although Johnson was a heavy-set, rough-looking, rude character who was still a bachelor at age 47, he had the reputation of a ladies' man. Due to a wound he received in Mexico, he was afflicted with an eye that winked uncontrollably, causing many women to believe he was flirting with them. He caused enough attention that he rated mentions in the famous diary of
Mary Chesnut.
Stonewall division In 1863, following the reorganization of the
Army of Northern Virginia to compensate for the death of Stonewall Jackson after the
Battle of Chancellorsville, Johnson was promoted to
major general and given command of the "Stonewall Division" in
Lt. Gen. Richard S. Ewell's Second Corps. Robert E. Lee had become dissatisfied with the previous commander at the battle and summoned Johnson back from medical leave to take the command.
Gettysburg By May 1863, Johnson had recovered enough to lead his division in the
Gettysburg campaign. He still needed a heavy hickory stick to move around on foot (and was known to use it against men he believed were shirking battle) and his men nicknamed him "Old Clubby". On the way north into
Pennsylvania as part of the left wing (under command of Ewell) that passed across the Shenandoah valley, Johnson's command participated in defeating
Union troops fortified at the city of
Winchester, commanded by Johnson's old nemesis Maj. Gen.
Robert H. Milroy at the
Second Battle of Winchester. Johnson arrived at the
Battle of Gettysburg on the evening of the first day, July 1, 1863. In a move that is still controversial, Ewell did not take advantage of Johnson's division and attack
Cemetery Hill immediately that evening, when it might have been decisive. Johnson controversially declined to attack
Culp's Hill that evening, for which he had a discretionary order. Instead, Johnson's division was the primary force that attacked Culp's Hill on the second and third days, suffering considerable casualties assaulting this impregnable position multiple times with no lasting success. In the fall of 1863, Johnson played a prominent role in the
Mine Run Campaign.
Later war service In the
Overland Campaign of 1864, Johnson fought well at the
Battle of the Wilderness and when Lt. Gen.
James Longstreet was seriously wounded there, Robert E. Lee considered Johnson as a replacement corps commander. During the
Battle of Spotsylvania Court House, on May 12, 1864, at the "Bloody Angle" section of the Confederate "Mule Shoe" defensive line, Johnson was captured along with Brig. Gen.
George H. Steuart, and most of Johnson's division. He was imprisoned for months at
Morris Island, off the coast of
Charleston, South Carolina, and was exchanged on August 3, 1864. He was sent west to join Lt. Gen.
John Bell Hood's
Army of Tennessee, where he commanded a division in the corps of Lt. Gen.
Stephen D. Lee. During the
Franklin-Nashville Campaign, Johnson was captured again at the
Battle of Nashville on December 16, 1864. He again spent months in a Union prisoner of war camp at
Johnson's Island, in
Lake Erie. At the end of the war, Johnson was moved to the
Old Capitol Prison in Washington, D.C., where he was accused of being somehow complicit in the assassination of
Abraham Lincoln. Nothing came of the accusation and he was paroled on July 22, 1865. ==Postbellum life==