Paper Mario: The Thousand-Year Door is a turn-based role-playing game and the second entry in the Paper Mario series, set in a world styled to look like paper. Players guide Mario through themed locations, solving puzzles and battling enemies in a timing-based combat system where well-timed button presses strengthen attacks and defense. Battles play out on a stage before an audience whose reactions can help or hinder the player, and Mario recruits a party of companions with unique skills while equipping badges that grant new abilities. Brief segments also let the player control Princess Peach and Bowser between chapters.

In the seaside town of Rogueport, Princess Peach acquires a mysterious treasure map said to point to a great fortune hidden behind the fabled Thousand-Year Door, sealed beneath ruins built atop a town that sank long ago. Peach sends the map to Mario, but she is soon kidnapped by an alien group called the X-Nauts who are after the same treasure. Mario travels to Rogueport and learns that the map reveals the locations of seven Crystal Stars needed to open the door. Gathering allies along the way, he sets out to collect the stars, rescue the princess, and uncover the secret of what lies behind the Thousand-Year Door.