The Skull Gem is an item held by Flavio during the events of Paper Mario: The Thousand-Year Door. It was originally owned by Cortez, and was used to operate his ship, the Black Skull. But, Flavio's ancestors stole it from Cortez, leaving the Black Skull unable to move. The Skull Gem got passed down from parent to offspring until the current generation, Flavio. When first met, Flavia can be seen in the Chuckola Cola bar with the Skull Gem on the table.
During chapter five, Flavio goes to Keelhaul Key with the Skull Gem alongside Mario and his friends. At the very end of Keelhaul Key, there is a wall that seperates Keelhaul Key and the Pirate's Grotto. The Skull Gem is needed to solve a puzzle that destroys the wall. Later in the chapter, when Mario and co. are attacked by Lord Crump, Flavio gets the idea to ask Cortez to use the Black Skull, and uses the Skull Gem to reanimate the ship.