Black Skull

The Black Skull is Cortez's pirate ship in Paper Mario: The Thousand-Year Door. It was permanently grounded long ago and docked deep in Pirate's Grotto until Mario and his partners came in and defeated Cortez. It turned out that the source of the Black Skull's power was the Skull Gem, which Flavio's ancestors stole from Cortez. Flavio agreed to give Cortez the Skull Gem in exchange for use of his ship, his own having been destroyed some time before. Soon after, Lord Crump attacks with the X-Ship and a second battle commenced between the X-Nauts and Cortez's army of Embers.

After the chapter, the Black Skull is docked in Rogueport and can take Mario to and from Keelhaul Key at any time; however, Mario can no longer go inside. This is equivalent to the Whale taking Mario to and from Lavalava Island in Paper Mario.

Trivia

 * It could be possible that the Black Skull is based on the Black Pearl from the Pirates of the Carribean. The Black Skull was "raised" from its resting place much like the Black Pearl was. Also, the Black Skull's owner could be based on the dread Davy Jones who was also in Pirates of the Carribean.
 * The Black Skull can also be a reference to The Flying Dutchman, since its captain is cursed to roam the seas, much like Cortez since he cannot leave his treasure.