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The Shadow Queen long ago came to the Mushroom World planning to throw it into a state of cataclysm and become its tyrannic ruler. However, the Shadow Queen's plans were ruined when four heroes sealed her away behind the Thousand-Year Door. The basis of Paper Mario: The Thousand-Year Door revolves around Sir Grodus's attempt at reviving her, with hopes of using her to take over the world.
Upon her release by Grodus and the Shadow Sirens, the Shadow Queen uses Princess Peach's body as a host. She then reduces Grodus to a incapacitated head for his less-than-respectful attitude, and the prelude to the final battle begins. Following a brief scuffle, the queen gives Mario and co. the "merciful" option of becoming her slaves in the post-cataclysmic Mushroom World. Accepting her offer results in a Game Over, but refusing continues the current battle. Following a massive power-up that makes the queen seemingly invincible, Mario realizes that he can't defeat her by himself. Calling upon the power of the seven Crystal Stars, the channeling of positive emotions by his friends and allies in Rogueport breaks the Shadow Queen's dark barrier and gives Mario and co. the opportunity to finish her off.
After Mario wins the battle, Peach is freed from the Shadow Queen's influence. The two then depart from Rogueport and return to the Mushroom Kingdom.