Harris, in command of the "Uncas", left New York for the Gulf Coast on February 28, 1862. Damage from a gale forced the ship to head for Hampton Roads, Virginia, for repairs and fuel; they arrived in time to witness the battle between the "Monitor" and "Virginia" (formerly the "Merrimack"). Because of the damage to the "Uncas", Harris was ordered to transfer his equipment and crew to its sister ship, the "Sachem", for the remainder of the voyage to the Gulf Coast. They left Hampton Roads on March 18 and stopped at Port Royal, South Carolina, for coal on the 24th. There, Harris was rebuffed by the Navy supply department and was instead ordered, under threat of facing a firing squad, to support an expedition to Edisto Island. Harris declined, repeatedly stating that he was under Coast Survey orders to proceed to Ship Island and report to Commodore Farragut. Only through the personal intervention of Commodore Samuel Francis Du Pont was the "Sachem" finally coaled and allowed to depart Port Royal. Following another coaling stop at Key West (during which four men mutinied and refused orders to pass coal to the vessel), Harris continued on to Ship Island and arrived April 9, to discover that the fleet had left the day before and gone to the mouth of the Mississippi River. The "Sachem" proceeded to the Mississippi River and arrived April 10, when Harris turned over command of the small steamer to Ferdinand Gerdes, who had arrived a few days earlier.