1861 – December 1862 In February 1861 he was the captain of the steamer
General Rusk and transported General
John Salmon Ford and his troops to the mouth of the Rio Grande to receive the surrender of Union Major
Fitz John Porter. Unattached to either side, Smith then contracted with Major Porter to transport the Union troops to New York. Smith reportedly replying to a hail from
Star of the West with "The General Rusk with troops on board. Can you take our line now ?" and explaining that the
Fashion would be arriving later with the luggage and the rest of the troops. The boarding troops promptly seized the
Star of the West at bayonet point. Between October 1861 and December 1862 Smith and the
General Rusk were under the command of CSN Commander William W. Hunter. On 7 November 1861, Smith and the
General Rusk extinguished the fire aboard the stricken
Royal Yacht following her encounter with , and towed her back to port.
December 1862 – January 1863: Appointment to command, Battle of Galveston Following the retreat from Galveston in the
Battle of Galveston Harbor (1862), General
Paul Octave Hébert was relieved from command and replaced in November 1862 by General
John B. Magruder who arrived in Texas. Previously acquainted with Smith, in December Magruder placed Smith in charge of all the steamers at his disposal. On Christmas Day 1862, Smith was charged with hastily improvising the , , along with the tenders
Lucy Gwinn and the
John F. Carr for battle as improvised
Cottonclad warships. The
Bayou City was outfitted with a single 32-pounder rifled cannon and the
Neptune with two 24-pounders howitzers. Cotton bales were used to provide a semblance of protection that was somewhat effective in stopping small arm fire, however when asked by a soldier about artillery protection Smith bluntly replied: "None whatsover... our only chance is to get alongside before they hit us". Boarding devices resembling the Roman
Corvus were placed on the hurricane deck of each boat. Facing Smith's forces were vastly superior Union naval forces: , , , , , , and four smaller vessels. The attack initially planned for 27 December 1862 was delayed to New Year's Eve, the
Battle of Galveston. Smith's force was to attack from sea into the Harbor as General Magruder attacked from land crossing over the railroad trestle connecting the island to the mainland. Smith was to wait to be signaled by gunfire that the battle had begun, which was expected to occur at midnight. However, Magruder's forces were delayed by the difficulty of crossing his artillery over the trestle. After no signal came after midnight passed, Smith pulled back from the harbor to Red Fish Bar, a point fourteen miles away. Hearing the attack commencing at 04:00, Smith directed the naval contingent back to the harbor, probably reaching it an hour after the initial shots were fired. Attacking just before daybreak, the CS
Neptune was severely damaged and sunk, but Smith, aboard the CS
Bayou City managed to ram into the
Harriet Lane, board, and capture her, reportedly personally killing US Navy Commander
Jonathan Mayhew Wainwright and recovering a valuable signal book. Though still outnumbered, Smith demanded the surrender of US fleet from commander
William B. Renshaw, who had run aground aboard the USS
Westfield. While under the flag of truce, Renshaw blew up his vessel and died in the explosion. Smith boarded the USS
John F. Carr and captured her as well, while the rest of the US Navy ships escaped to sea. Aboard the captured USS
John F. Carr, Smith gave chase to the fleeing Union ships, however the small ship was unable to match the speed of the larger warships. Turning around back to the bay, Smith captured three small Union ships (the
Cavallo,
Elias Pike, and
Lecompte) with their cargo. Following the battle, Smith won praise for his gallant conduct, including a mention in a joint resolution of the
Congress of the Confederate States. General Magruder attempted to secure a regular Naval commission as
commander for him, one of several repeated attempts, which did not result in an actual commission being granted.
January 1863 – August 1864 Following the battle, the
Confederate States Navy sent Lieutenant
Joseph Nicholson Barney to take charge of naval operations in Galveston, including the captured
Harriet Lane. However, after discussions with Magruder who was not willing to relinquish control of the cottonclads, Barney conceded the appointment, and in a letter to
Confederate naval secretary Stephen Mallory recommended that the Navy relinquish control. Barney later explained that he made his recommendation since he considered that the presence of two separate marine forces with independent commanders would lead to discord and confusion. From November to December 1863, he was sent by Magruder to direct the naval side of the defense of
Indianola, Texas, where Colonel William R. Bradfute was commanding the land forces. As part of the engagement, the Confederates retreated in the
Battle of Fort Esperanza. Smith commanded
John F. Carr,
Cora, and eleven small vessels with sharpshooters and artillery; however disagreements with Bradfute were a hindrance to operations. Smith chose not to take the offensive, fighting defensively. In early 1864 Brig. Gen.
William Steele, who was given command of Galveston, attempted to take control of the naval forces there, however Magruder asserted Smith's authority. who commanded the marine department sub-district at Galveston. Smith was ordered by Magruder to report "by letter" to the
Confederate States Secretary of the Navy. Smith, however, did not depart Texas immediately, and in September 1864 he captured the US schooner
Florence Bearn at the mouth of the Rio Grande. In November 1864 he was in
Havana where his presence was noted by Union officials, and where he was detained by Spanish authorities for a time. He subsequently piloted the steamer
Wren to Galveston through the Union blockade. In an April 1865 letter Magruder writes that Smith will bring in a valuable Confederate steamer probably in the next dark moon. On 20 June 1865 he reportedly left Texas with other notable Confederate figures. ==Post–Civil War==