Under the command of Lieutenant F. M. Harris, the schooner was part of a nine-gunboat naval squadron tasked with the defense of the northeastern North Carolina sounds. She was at anchor in Croatan Sound under the guns of Fort Forrest when a Union army/navy force under the command of General Ambrose Burnside arrived on February 6, 1862 to invade Roanoke Island. Burnside sent his forces to destroy the remains of the Southern Mosquito Fleet still operating in North Carolina's sounds.
Late in the day the Black Warrior was detailed to salvage what guns and ammunition she could from the partially sunk gunboat Curlew. That evening the squadron retreated to Elizabeth City to obtain more ammunition. One of the gunboats, the Ellis, took the Black Warrior in tow while the remainder of the squadron made their way overnight to Elizabeth City.