Chapter 8

After Mario has received all seven Crystal Stars, the time has come to open the Thousand-Year Door and enter the Palace of Shadow to rescue Princess Peach from Grodus.

Mario and his friends open the Thousand-Year Door with the seven Crystal Stars, allowing them to enter the Palace of Shadow. The palace itself is full of enemies, puzzles, and traps. Eventually, Mario and co. battle and trounce the Shadow Sirens and a black dragon named Gloomtail, older brother of Hooktail. After the dragon's defeat, he relinquishes the key to access the Riddle Tower. After solving the puzzles of the tower, a secret passage is revealed, which lets Mario continue forward. Finally, Mario reaches the Throne Room of the palace, where he finds and defeats Sir Grodus. Bowser and Kammy, who drop in unexpectedly, also battle Mario, but are thwarted in the end. Grodus uses the distraction of the battle to bring the Princess into the deepest part of the palace. There, he opens a sealed coffin and frees the Shadow Queen, the ancient demon of legend. Beldam suddenly appears and announces that she was the one who orchestrated the plot to free her mistress. The Shadow Queen refuses to be controlled by Grodus, and fries him with a lightning bolt, supposedly killing him. The Queen then possesses Princess Peach, using her as a vessel to sustain her life. The world is then covered in darkness. Mario and his allies fight the Queen, but she eventually decides to fight in her real form, in which she is invincible. She proves too much for the group to handle, however, the Crystal Stars suddenly react to the evil of the Queen and fly throughout the world, each returning to where they were found, allowing the people of the world to cheer on Mario and his party. The hope of the people of the world break through the Queen's invulnerability, and this also allows Peach to give the heroes the last of her power. Strengthened, the heroes seal the Shadow Queen forever, saving the world.

Goombella later sends Mario a message, explaining what everyone has done: she works with Professor Frankly, while Koops plans on becoming the Mayor of Petalburg. Flurrie has returned to the stage and enacts "Paper Mario" as her comeback smash while Doopliss plays the role of Mario. The Yoshi Kid fights in the Glitz Pit as the "Great Gonzales Jr.", while Vivian has forgiven her sisters and lives in Twilight Town. Admiral Bobbery sails the seas with Cortez, and Ms. Mowz runs her Lovely Howz of Badges. Lord Crump, Grodus and the X-Nauts survived and are spending their time in Poshley Heights. TEC survived as well, and hopes to see the Princess again one day. The game ends when the Princess arrives with another treasure map.