The Black Skull is Cortez's pirate ship in Paper Mario: The Thousand Year Door. It was docked in Pirate's Grotto until Mario and his partners came in and defeated Cortez. Soon after Lord Crump came with his ship and a second battle commenced between Cortez's army of Embers and the X-Nauts.
After the chapter, the Black Skull is in Rogueports docks and can take Mario to and from Keelhaul Key. This is basically the same as the Whale taking Mario to and from Lavalava Island in Paper Mario.