After the end of the Civil War, Thomas commanded the Department of the Cumberland in Kentucky and Tennessee, and at times also West Virginia and parts of Georgia, Mississippi and Alabama, through 1869.
President Andrew Johnson offered Thomas the rank of lieutenant general-with the intent to eventually replace Grant, a Republican and future president, with Thomas as general in chief-but the ever-loyal Thomas asked the Senate to withdraw his name for that nomination because he did not want to be party to politics.