The mysterious organization in Paper Mario: The Thousand-Year Door is called the X-Nauts. They are the principal enemy group working to unlock the Thousand-Year Door and revive the ancient Shadow Queen.
The X-Nauts are led by Sir Grodus, with Lord Crump acting as one of the organization’s most persistent field agents. Their plan centers on collecting the seven Crystal Stars, which are needed to open the Thousand-Year Door beneath Rogueport. They also kidnap Princess Peach because they intend to use her as a vessel for the Shadow Queen.
The group’s name and design give them a deliberately strange, almost extraterrestrial appearance. Their headquarters, technology, uniforms, and military hierarchy help make The Thousand-Year Door feel different from a typical Bowser-led Mario plot.
Shy Guys, Hammer Bros, and Koopas are recurring Mario species or enemy types, not the organization behind this game’s main conspiracy. The X-Nauts are also distinct from the Shadow Sirens, another villainous group that serves the same larger resurrection scheme.