Johnston returned to the field in November 1862 and was placed in command of Confederate forces in the war’s Western Theater. In May 1863 he was ordered to take charge of operations in Mississippi, which was threatened by forces under the command of Union General Ulysses S. Grant. After abandoning the state capital of Jackson, Johnston attempted to rendezvous with General John C. Pemberton, who was besieged at the vital Mississippi River hub at Vicksburg. Recognizing that he was at a severe numerical disadvantage, Johnston ordered Pemberton to cede the city to Union control. Pemberton, however, was under orders from Jefferson Davis to hold the city to the last, and refused to evacuate. Believing he didn’t have enough troops to mount an offensive and break the siege, Johnston elected not to attack Grant. Pemberton’s army was forced to surrender on July 4, 1863, and control of Vicksburg fell to the Union.
Johnston was widely condemned for his overly cautious tactics in Mississippi, but in November 1863 he took command of the Army of Tennessee after General Braxton Bragg was relieved from duty. Tasked with halting General William T. Sherman’s march from Tennessee toward Atlanta, Johnston continued his policy of strategic retreat, which he believed preserved his army and allowed him to maneuver into strong defensive positions. This plan proved largely unsuccessful, as Sherman expertly bypassed Johnston’s army and inched closer toward Atlanta throughout May 1864. While Johnston succeeded in striking a blow against Sherman at the Battle of Kennesaw Mountain in June 1864, his reluctance make a decisive stand agitated Jefferson Davis, who replaced him with General John Bell Hood a month later.
Johnston was reinstated in February 1865 and took command of the battered Army of Tennessee, which was assembled in North Carolina to delay Sherman’s march north after the fall of Atlanta. Working with General P.G.T. Beauregard, Johnston attempted a surprise attack at the Battle of Bentonville in March 1865, but was overwhelmed by a force three times the size of his own. After falling back to Greensboro, North Carolina, Johnston and Beauregard surrendered in late April 1865 after learning that Robert E. Lee had capitulated several days earlier at Appomattox.