Just before the start of the Civil War, Thomas was promoted to colonel and adjutant general of the U.S. Army on March 7, 1861. On August 10, 1861, U.S. President Abraham Lincoln appointed Thomas a brigadier general in the regular army, to rank from August 3, 1861, the date Lincoln sent the nomination to the U.S. Senate for confirmation. The Senate confirmed the appointment on August 5, 1861. Camp Thomas, a Regular Armytraining base in Columbus, Ohio, was named in his honor in July 1861. He held the position of adjutant general until he retired in 1869, except for a special assignment to recruit African-American troops in the Military Division of the Mississippi from 1863 to 1865. Thomas did not get along well with Secretary of War Edwin M. Stanton and this assignment outside of Washington, D.C., was considered a form of banishment. Many historians have claimed Thomas was banished in disgrace after conspiring to defame Union General William T. Sherman as insane. Thomas was replaced by Maj. Gen. Edward D. Townsend as Adjutant General, who would serve until 1880. From March 17 to July 23, 1862, he served as the chairman of the War Board, the organization that assisted U.S. President Abraham Lincoln and Secretary Stanton in the management of the War Department and the command of the Union armies during the period in which there was no general-in-chief. On April 6, 1863, General Thomas was sent by the War Department to Helena, Arkansas to recruit freedmen into the U.S. Army. He created the first black troop in Arkansas, fighting for Union side as part of Bureau of Colored Troops, which was created by the War Department on May 22, 1863. On March 8, 1866, U.S. President Andrew Johnson nominated Thomas to the grade of brevet major general in the regular army, and the U.S. Senate confirmed the appointment on July 14, 1866.
Postbellum career
On February 21, 1868, President Johnson attempted to replace Stanton by appointing Thomas as Secretary of War ad interim. Thomas, still stinging from his bad treatment by Stanton, boasted of his ability and determination to oust him from office by force, if necessary. Some historians believe that it was this attitude in his testimony at Johnson's impeachment trial in the Senate that was partially responsible for Johnson's acquittal. Thomas retired from the Army on February 22, 1869, ten days before Johnson left office. He died in Washington, D.C., and is buried in Oak Hill Cemetery, Georgetown. Fort Thomas, a military post established in Arizona Territory in 1876, was named for Thomas.
