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.