Sora, Donald, and Goofy have almost reached the 13th floor of Castle Oblivion. They find themselves in a long white hallway. Sora stops and pulls out his good luck charm, asking himself who the most important person to him is. No matter how hard he stares at it, he can't remember her name, and neither can Donald and Goofy. Before they proceed, they promise to remain friends forever, no matter what happens to them.
As the trio nears the top of the castle, Axel appears to confront Marluxia. He calls Axel a traitor for letting Naminé escape, thus ruining his plan. Axel recounts what their plan was: by having her tamper with Sora's memories, he and Larxene would turn Sora into Naminé's puppet, and by extension their puppet since they controlled Naminé. With the power of the Keyblade on their side, the two of them had hoped to overthrow the leader of the Organization and seize power for themselves. Axel tells Marluxia that if anybody is a traitor, it's him. Marluxia asks him when he started to suspect their treason, but Axel says he never trusted them to begin with due to his lack of a heart. Axel confirms that he only killed Vexen to obtain their trust and undermine their plan from within. As Axel brandishes his chakrams, he reminds Marluxia of the order that he himself gave: Eliminate the traitor. With that, the two of them begin to fight.
As they battle, Axel goes on the offensive, but Marluxia blocks his attacks with ease; nevertheless, Axel manages to defend against Marluxia's own strikes. With the battle at a stalemate, Marluxia tries to turn the tide by teleporting Naminé to himself to use as a shield. Axel mocks him, saying that he has no qualms with harming Naminé, but Marluxia reveals that the shield wasn't to stop Axel; it was to call Sora to action. To Axel's surprise, Sora, Donald, and Goofy have already made it to the room they are in. Axel calls Sora a puppet for Marluxia, but he says the Graceful Assassin is his next opponent after dealing with him. Axel says he doesn't really want to fight Sora, but he's left with no choice. Sora defeats Axel, who says that it was worth it to save him. Sora asks what he means, but Axel refuses to answer. He fades away, seemingly being destroyed like Vexen and Larxene. After defeating him, the trio continues.
The group finally reaches the 13th floor, where they find Marluxia and Naminé in a long hallway with a door at the end. Marluxia tells Sora of his ambition to gain the power of the Keyblade for himself. He orders Naminé to completely erase Sora's memory, which would destroy his heart. Marluxia explains that this would damage Sora, which he would have rather avoided, but as a mindless puppet, he can eventually be rebuilt as his slave. Naminé, refuses to obey him, telling Marluxia about Sora's kindness and forgiveness. Sora, however, tells Naminé to do it so she can be spared from Marluxia's wrath. He tells her that even if he loses his memories, they can still defeat Marluxia, and afterwards Donald and Goofy can help him regain them.
Marluxia tells Sora that if his memories are erased, he'll end up as a mindless puppet just like the Riku Replica. Suddenly, the replica jumps out and attacks Marluxia. He manages to dodge the hit, but it separates him from Naminé. Marluxia tells him that he lost everything, but the Riku Replica says he had nothing to lose in the first place...except for the promise he made to protect Naminé. Just like Sora, the replica says that even if his promise is fake, he still plans to honor it. Marluxia summons his scythe calls them fools for openly embracing false memories, proclaiming that they will never defeat him.
After a fierce battle, the group seemingly defeats Marluxia; however, he reveals that it was just an illusion. Marluxia appears, and the Riku Replica charges at him, but it turns out to just be another illusion, which promptly vanishes. Naminé tells them that the real Marluxia is inside the door. Sora tells the Riku Replica to look after Naminé while he ends onward. After some final preparations, Sora opens the door and heads inside.
Inside the door, Sora finds himself in a world of nothingness, which Marluxia plans to use to destroy his heart. He summons a big scythe mech, but even it proves to be no match for Sora. After Sora destroys the mech, Marluxia fights him directly with the assistance of a giant Grim Reaper apparition. Despite all of his immense power, Sora emerges victorious. Marluxia screams in rage and tries to reach out to grab Sora before ultimately fading away.
After defeating Marluxia, Sora returns to the hallway. Donald and Goofy close the door, and Sora quickly seals it with the Keyblade to prevent Marluxia from ever returning. Sora asks "Riku" if he's OK, but the replica insists that he not be called Riku since he's a fake. He says that all he has are his fake memories of Sora and Naminé. Goofy asks Naminé if she can restore the Riku Replica's memories to normal, but he insists that they not worry about him. Sora tells him that even if he was created to be a copy of someone else, he is his own person with his own heart and identity. The Riku Replica thanks Sora for his kind words and leaves.
After the replica leaves, Naminé explains that she never actually erased any memories, but rather merely "unchained" them. They still exist within their hearts, and she simply has to put the chain of memories back together. Before she can do that, though, she has to remove the memories she created. She explains that removing the fake memories and reconnecting the real ones may take quite a while, but it's the only way to return them to normal. Jiminy comes to the realization that, if Naminé has to remove the memories she created, that means they'll forget everything that happened since the end of their last adventure, when they closed the Door to Darkness and found Pluto in the field. Naminé offers Sora a choice: he can regain his old memories at the cost of losing his memories of Castle Oblivion, along with having to wait for a long time to have them put back together, or he can keep his current memories and forget what happened before.
Sora chooses to regain his old memories, to Naminé's disappointment. She leads them to another chamber that contains a huge pod. She explains that they have to sleep in the pod until their memories are restored. Donald asks how they'll thank her for repairing their memories. Jiminy writes a message, "Thank Naminé," in his journal, so they can remember even when they wake up. Donald and Goofy go to their separate pods to sleep, saying "goodnight" to Naminé.
Naminé tells Sora that, even though their relationship was founded on a lie, she's still glad to have met him. Sora says that even so, the feelings he felt for her were not lies. She tells him "goodbye," but Sora says it won't be a "goodbye;" when he wakes up, he plans to be friends with her for real. Sora makes a promise to see her again. Even though Naminé says he'll forget it, Sora reminds her that even if he does forget, it will still be inside his heart somewhere. Naminé smiles and agrees to make the promise. As Sora jumps into the pod, she tells him that some of his memories are in the shadows of his heart. Even though she can't find them, there is someone else who will help him remember. Naminé tells Sora that as long as he remembers her and the promise he made to her, he can regain all his memories. She tells him to look at the good luck charm again, reminding him that it turned back to normal on Destiny Islands. Sora clutches the charm and looks down at it as the pod closes shut. Once it's closed, Sora has a vision of all his friends, including Kairi, whose name he finally remembers. A light shines as he says her name. As Naminé fades away, she tells him that as long as they have their promise, they will meet again someday.
Meanwhile, the remaining members of the Organization are meeting in a round room full of chairs. Their leader, who sits upon the highest chair, has been keeping a close eye on everything that has happened in Castle Oblivion. As Naminé watches over the pods, Sora's story ends with a poem:
"There is always sleep between part and meet
with our usual words on the usual street
So let us part like we always do...
And in a world without you
I'll dream of you.
When I come to, let us meet
with our usual words on the usual street."
