Sora, Donald and Goofy walk down a long path that seemingly goes nowhere. where they meet and follow Pluto, who leads them to a crossroads. Here, a man in a black cloak approaches Sora and speaks to Sora, but at that moment his words are incomprehensible. The path then becomes one and it leads them to Castle Oblivion. The cloaked man appears as they enter the castle and gives them a card. They use the card to proceed through the castle. The first world they go to is Traverse Town, where they discover that Leon, Aerith, Yuffie, and Cid have forgotten all about them, yet they strangely remember Sora's, Donald's, and Goofy's names, where Yuffie comments, "You're not in my memory, but my heart remembers you." After Leon gives Sora a tutorial on fighting, they leave Traverse Town. The man appears once more after they arrive on the next floor. Another cloaked man appears and introduces himself as Axel. Sora battles him and when defeated, Axel gives you more cards, disappearing soon after. Sora, Donald, and Goofy go through each floor, experiencing their memories, among the castle floors. They start to lose their memories. A Nobody named Naminé begins to replace memories of Kairi with fake ones of herself. It turns out she is good and is manipulating his memories under the orders of the head of the castle, Marluxia. This escalates to a final battle in the end, for Sora's life, and Naminé's freedom.
Meanwhile, Riku awakens down in the castle, and as he goes up the basement levels of Castle Oblivion, he must take control of the inner darkness inside of him, dealing with Xehanort's Heartless, the Riku Replica, and three members of Organization XIII, Vexen, Lexaeus, and Zexion, along the way.
- Castle Oblivion: Bosses: Axel, Larxene, Marluxia, Riku, Lexaeus, Xehanort's Heartless, Vexen.
- Traverse Town: Boss: Guard Armor.
- Wonderland: Bosses: Card Soldiers, Trickmaster.
- Olympus Coliseum: Bosses: Cloud Strife, Hades.
- Agrabah: Boss: Jafar.
- Hollow Bastion: Boss: Maleficent.
- Halloween Town: Boss: Oogie Boogie.
- Monstro: Boss: Parasite Cage.
- Destiny Islands: Bosses: Darkside, Zexion (Re:Chain of Memories only).
- Neverland: Boss: Captain Hook.
- Atlantica: Boss: Ursula.
- Twilight Town: Bosses: Vexen, Riku Replica
Reverse Rebirth Edit
After completing the game as Sora, Reverse/Rebirth mode follows Riku as he climbs the basements of Castle Oblivion. Riku's deck cannot be changed, however, it changes automatically as time goes on. Riku does not need as much time to reload his deck. Certain enemy cards are only available to Riku, and then unlocked for Sora after completing the game with Riku. Riku can only keep the enemy cards that are based off of the bosses after winning them during battle, the others are available in one world only.