Randolph
The USS Randolph was one of the first ships built for the Continental Navy, and later became its flagship.
The Randolph was finished in 1776, and staffed by British prisoners. It set sail in February 1777, but ended up in Charlestown with broken masts and its crew decimated by the fever. On top of that, the British crew had attempted a mutiny.
During the repairs, the masts were hit by lightning twive, slowing the process of preparing the Randolph for its journey, and it only began its military career in August 1777. By that time, it was captained by Nicholas Biddle, a Templar who used it to aid the Templar cause and raid ships along the East Coast.
The Assassin Connor, captain of the Aquila, eventually chased the Randolph down and managed to destroy its masts, allowing his crew to board the ship. He then fought and defeated Biddle, who begged him not to take the ships as a prize. Connor decided to sink the ship, allowing Biddle to sink with it.