Service in the Western Theater On the recommendation of
Simon Bolivar Buckner, the former commander of the Kentucky State Militia who had also joined the Confederate Army, Breckinridge was commissioned as a
brigadier general on November 2, 1861. On November 16, he was given command of the 1st Kentucky Brigade. Nicknamed the
Orphan Brigade because its men felt orphaned by Kentucky's Unionist state government, the brigade was in Buckner's 2nd Division of the
Army of Mississippi, commanded by General
Albert Sidney Johnston. For several weeks, he trained his troops in the city, and he also participated in the organization of a provisional
Confederate government for the state. Although not sanctioned by the legislature in Frankfort, its existence prompted the Confederacy to admit Kentucky on December 10, 1861. Johnston's forces were forced to withdraw from Bowling Green in February 1862. During the retreat, Breckinridge was put in charge of Johnston's Reserve Corps. After his promotion, he joined
Earl Van Dorn near
Vicksburg, Mississippi. Breckinridge asserted to his superiors that Bragg's report "fails to do justice to the behavior of my Division"; he requested a court of inquiry, but the request was denied. Several Kentuckians under Breckinridge's command, who already blamed Bragg for the failed invasion of their native state, encouraged him to resign his commission and challenge Bragg to a duel. In May 1863, Breckinridge was reassigned to Joseph E. Johnston, participating in the
Battle of Jackson in an unsuccessful attempt to break the
siege of Vicksburg. Confederate leaders were skeptical of Bragg's claims against Breckinridge, and in February 1864,
Confederate President Jefferson Davis assigned him to the
Eastern Theater and put him in charge of the Trans-Allegheny Department (later known as the
Department of East Tennessee and West Virginia). Shortly thereafter, Breckinridge's Division reinforced Lee's
Army of Northern Virginia and played an important role in halting Grant's advance at the
Battle of Cold Harbor. In mid-November, Breckinridge led a raid into northeastern Tennessee, driving
Alvan Cullem Gillem's forces back to
Knoxville at the
Battle of Bull's Gap. On December 17–18, he faced a two-pronged attack from Union cavalry under Major General
George Stoneman at the
Battle of Marion in Virginia. Badly outnumbered on either flank, Breckinridge resisted Stoneman's forces until he ran low on ammunition. Stoneman's forces were able to damage Confederate salt works, lead mines, and railroads in the area, and destroy supply depots at
Bristol and Abingdon. Finally restocked with ammunition after three days, Breckinridge was able to drive Stoneman – whose men were now short of ammunition themselves – out of the area.
Confederate Secretary of War James A. Seddon resigned his position as the Confederate Secretary of War on January 19, 1865. On February 6, Davis appointed Breckinridge to the vacant position, partially to quiet growing opposition to his administration. Initially opposed by several members of the
Confederate Congress because he had waited to join the Confederacy, he eventually gained their support by administering his office more efficiently than his predecessors. With their support, he was able to expand the post's influence to include making officer assignments and promotion recommendations and advising field generals regarding strategy. His first act as secretary was to promote Robert E. Lee to general-in-chief of all Confederate forces. After Lee reported a critical shortage of food, clothing, and supplies among his troops, Breckinridge recommended the removal of
Lucius B. Northrop, the Confederate
commissary general. Northrop's successor,
Isaac M. St. John, improved the flow of supplies to troops in the field. in downtown Lexington By late February, Breckinridge concluded that the Confederate cause was hopeless. Delegating the day-to-day operations of his office to his assistant,
John Archibald Campbell, he began laying the groundwork for surrender. Davis desired to continue the fight, but Breckinridge urged, "This has been a magnificent epic. In God's name let it not terminate in farce." On April 2, Lee sent a telegram to Breckinridge informing him that he would have to withdraw from his position that night, and that this would necessitate the evacuation of Richmond. Ordering Campbell to organize the flight of the Confederate cabinet to
Danville, Virginia, Breckinridge remained in the city to oversee the destruction of facilities and supplies to prevent their use by the invading federal forces. However, he did not destroy Confederate archives and records, which were preserved for history. Upon his exit from the city, he ordered that the bridges over the
James River be burned. His son Clifton, then serving in the
Confederate Navy at Richmond, resigned his post and joined his father as he moved southward to meet Davis. After overseeing the transfer of Richmond, Breckinridge joined Lee's forces at
Farmville, Virginia, on the night of April 5 and remained there until April 7. He continued on to Danville, arriving on April 11 to discover that
Lee had surrendered on April 9 and the Confederate cabinet had already fled to
Greensboro, North Carolina. Arriving in Greensboro on April 13, he advised the cabinet that the remaining Confederate armies should be surrendered; only Davis and Secretary of State
Judah P. Benjamin disagreed. At
Bennett Place, he assisted Joseph E. Johnston in his surrender negotiations with Major General
William Tecumseh Sherman. Sherman later praised Breckinridge's negotiating skills, and the surrender terms agreed to were later rejected by Washington as too generous, forcing Sherman to offer the same terms as Grant had at Appomattox, which were accepted. On April 18, Breckinridge heard from Sherman and Johnston of the
assassination of Abraham Lincoln four days earlier; the President had died in the
Petersen House, where Breckinridge briefly resided in late 1852 as a U.S. representative. The Kentuckian was visibly devastated. Eyewitness accounts recall him to have said, "Gentlemen, the South has lost its best friend." Breckinridge rode into
Abbeville, South Carolina, on the morning of April 28. While there, Breckinridge and Brigadier General
Basil W. Duke convinced Davis that continuing the war was hopeless. Breckinridge was put in charge of the $150,000 in gold specie remaining in the Confederate treasury; traveling southward by rail toward
Washington, Georgia, a group of soldiers in his military escort – unpaid for months – threatened to divide the gold among themselves before it could be captured by federal troops. Breckinridge convinced them to abandon their scheme after paying them their wages from the treasury, but some of them refused to escort Breckinridge and the bullion any further. Breckinridge's party arrived in Washington on May 4 and, after paying out several requisitions from the treasury, deposited the rest in banks there. He also composed a letter to his remaining deputies in which he disbanded the War Department. ==Escape and exile==