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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 turns out that the source of the Black Skull's power is the Skull Gem, which Flavio's ancestors have stolen from Cortez. Flavio agrees to give Cortez the Skull Gem in exchange for use of his ship, his own having been destroyed before. Soon after, Lord Crump attacks with the X-Ship and a second battle commences between the X-Nauts and Cortez's army of Embers. The ship has only two rooms: the room before the treasure room, that is where Cortez keeps all of his provisions and the treasure room, where he is first introduced.
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.
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