Twilight and Princess Peach are having themselves a princess vacation in a faraway land, starting in the ragged port city, Rougeport. They find a mysterious treasure map given to them by a mysterious trader, and not wanting to leave their friends out on discovering something exciting, they deliver letters to both Mario and Twilight's friends in Equestria, detailing their findings along with sending the map to the heroic plumber in red, and the gang set off to Rougeport to join the two princesses.

A far more dangerous game is afoot than Bowser's almost successful attempt months prior with the power of the Star Rod. A new enemy stands in their way, wanting to discover what lies beneath the port city, and they will do anything to open what is known as the legendary One Thousand Year Door. Not only that, but they have also managed to kidnap both Peach and Twilight, taking them hostage while the leader of this new group plans to uncover what secrets are hidden beyond this millennial doorway. Will Mario and co. be able to surpass this new foe and claim the treasure for themselves, or is there something far more sinister lurking deep below the land that could wreak havoc on the world?