Black Skull

The Black Skull is Cortez's pirate ship in Paper Mario: The Thousand-Year Door. It is permanently grounded long ago and docked deep in Pirate's Grotto until Mario and his partners come in and defeat Cortez. It turns out that the source of the Black Skull's power is the Skull Gem, which Flavio's ancestors has stole from Cortez. Flavio agrees to give Cortez the Skull Gem in exchange for use of his ship, his own having been destroyed before in some time. Soon after, Lord Crump attacks with the X-Ship and a second battle commences 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 film franchise. The Black Skull is "raised" from its resting place much like the Black Pearl is.
 * 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.