Mario
Mario is the protagonist of The Thousand-Year Door, having visited the city of Rogueport after getting a letter from Princess Peach, who becomes kidnapped by the enemy organization, the X-Nauts. On his quest, he allies with multiple characters, including the Goomba Goombella, the Koopa Troopa Koops, a woman named Flurry, a Yoshi, a woman named Vivian, and a Bob-omb named Bobbery, using his and their abilities to make progress in collecting the seven Crystal Stars to prevent the game's antagonist, Sir Grodus, from using them to open the Thousand-Year Door and releasing a great evil. After collecting all seven Crystal Stars, the X-Nauts manage to use them to open the door, unleashing the Shadow Queen, who Peach was kidnapped to serve as a host for. Mario successfully defeats her in the end, saving Peach in the process.
Partners
- Goombella
Goombella is a Goomba archaeologist student [4] and Mario's first partner, who joins him after being saved by him, as well as her archaeological interest in the Crystal Stars. She is able to provide an explanation for every character, enemy, and location in the game.
- Koops
Koops is a Koopa Troopa who sets out on a quest to defeat the dragon Hooktail who ate his father, much to the chagrin of his girlfriend. He joins Mario after discovering that he was going to Hooktail's Castle, and after they defeat Hooktail and recover a Crystal Star, they also discover his father, having survived in Hooktail's stomach. Koops is able to launch himself in his shell at enemies and objects, the latter able to be grabbed for Mario.
- Flurrie
Flurrieis an actress who assists Mario on his quest in order to help him access the Great Tree in Boggly Woods. She is a cloud spirit, capable of blowing hard enough to blow enemies and certain objects away.
- Yoshi
Mario receives an egg in the third chapter of the game, which eventually hatches into a Yoshi that quickly joins his party. Depending on how long it took for the player to progress in chapter 3, he will have a different color. The player can also choose to name him. He participates in a fighting tournament with Mario, naming himself The Great Gonzales Jr. after Mario's stage name. He is able to eat certain enemies and spit them out as projectiles.
- Vivian
Vivian initially serves as a member of the villainous Shadow Sirens, facing abuse from her older sister Beldam. In the original English version, Vivian was insulted for being ugly; in the Japanese version, she was insulted for being a transgender woman. This was restored in English in the 2024 remake of The Thousand-Year Door. This abuse, combined with Mario helping her find a lost object, eventually convinces Vivian to become Mario's ally. She has the ability to hide in shadows and take others into there with her.
- Adrmiral Bobbery
Admiral Bobbery is a Bob-omb sailor [4] who, after his wife passed away from illness while he was at sea, refused to sail again due to blaming himself for being absent. He eventually agrees to navigate a ship after Mario delivers a letter she wrote before her death, encouraging him to not give up on sailing. Like other Bob-ombs, Bobbery is capable of exploding to damage opponents and destroy certain things like cracked walls, though unlike most other Bob-ombs, he does not die from doing so.
- Ms. Mowz
Ms. Mowz is an optional playable character who runs a badge shop and acts as a thief otherwise. She is seen multiple times stealing treasure, giving a kiss to Mario each time they met. The player is able to add her to the party after finishing multiple optional quests. She is able to use her nose to discover treasure and steal items from enemies.
