Shortly after the Civil War began, Williams was promoted to major in the 5th U. S. Artillery on May 14, 1861. On September 28, 1861, President
Abraham Lincoln promoted Williams to Brigadier General of U. S. Volunteers, to rank from that date and on February 3, 1862, the U.S. Senate confirmed his nomination. He was posted to the command of a
brigade on the
Potomac River, and was later posted to Fort Hatteras, North Carolina. He then was assigned to Maj. Gen.
Benjamin Butler's command in the land operations against
New Orleans, Louisiana. Williams and his
brigade were assigned the task of occupying
Baton Rouge. On May 29, General Williams arrived in the city with six
regiments of
infantry, two
artillery batteries, and a troop of
cavalry. During the early summer, Williams' 3,000-man infantry brigade began work on what later became known as
Grant's Canal, cutting a new channel across the base of
De Soto Point on the west side of the
Mississippi River across from
Vicksburg, Mississippi. The purpose of the canal was to develop a channel for navigation that would enable
gunboats and transports to bypass the Confederate batteries at Vicksburg. In August 1862,
Confederate forces under the command of General
John C. Breckinridge attacked the Union defenses of Baton Rouge in an effort to retake the state's capital. In the resulting engagement, the
Battle of Baton Rouge, Williams was killed by a gunshot wound to his chest on August 5, 1862, while leading what proved to be the successful defense of the city. It was rumored that it was friendly fire. Williams's body was aboard the
transport steamer Whiteman or
Lewis Whitman (sources differ) along with other dead and wounded from the Battle of Baton Rouge when the steamer sank in the
Mississippi River near
Donaldsonville, Louisiana, with the loss of all hands after colliding with the
United States Navy sloop-of-war on August 7, 1862. A bronze memorial plaque was dedicated to Williams on August 12, 1907, at Fort Mackinac, with the dedication led by the Bishop of Michigan,
Charles David Williams. The plaque, located at the top of the ramp near the entrance by the South Sally Port, reads: “In Memory of General Thomas Williams, Commandant of Fort Mackinac, 1852-1856, Killed in Battle, August 5, 1862.” ==Personal life==