Appointed as a major in 1861, Williams was promoted to brigadier general in November 1861. He served as the inspector general of the Department of Virginia before he was sent on the October 1861 expedition to North Carolina. Williams was in charge at Fort Hatteras until March 1862 and was transferred to the command of General Benjamin Butler in New Orleans, Louisiana, and commanded the occupation of Baton Rouge in July 1862. He was killed in a Confederate attempt to recapture the town in August.
