Sora, Donald, and Goofy use the new World Card Vexen gave them. They step through the door to find a strange sight: it leads them to a place they've never been to, a world called Twilight Town. None of them can understand how they ended up there, since all the other World Cards led them to places they had seen before. Donald assumes that Sora has actually been there, and that he simply had his memories of it erased like everything else. Sora pulls out "Naminé's" good luck charm and says that they'll be alright as long as they have it. Sora recounts another childhood memory: when he and Naminé were kids, there was a meteor shower. Naminé got scared and asked Sora what they would do if a shooting star fell onto the islands, to which Sora responded by saying he'd knock it out of the sky with a wooden sword. Naminé then supposedly gave him the charm. In another vision, Naminé appears behind Sora and apologizes, saying she caused all this trouble. Sora continues the story: Naminé had the charm ever since she was a baby, and Sora thanked her by promising to be her new good luck charm—in other words, he would protect her. Recounting all those memories, Sora feels very guilty for forgetting about her.
The trio continues through the mysterious town until they reach the gates of an old mansion. Despite having never been there, Sora feels like he knows the place. Donald and Goofy assume it's just another one of Sora's deeply-buried memories like those of Naminé, but he denies it, saying this feeling is different. Suddenly, Vexen appears. He asks Sora whether his memories of Naminé or the mansion are more real. Sora naturally says his memories of Naminé are real, assuming his memories of the mansion to be a trick. Vexen laughs and tells Sora what he said before: the illusion of Twilight Town is made from the other side of his heart. He further tells Sora to listen to his heart, not the warped memories in his head. He compares Sora to "his" Riku, saying that they both have twisted memories. Sora decides that he's had enough of Vexen's mind games and prepares to fight.
The battle between Sora and Vexen is fierce, but ultimately Sora emerges on top once more. He demands Vexen return Riku to normal, but he simply says that Riku's fate is to be swallowed by darkness. He then warns Sora to stop chasing after Naminé, saying that he'll become a pawn of Marluxia if he doesn't stop. Before Sora can get any more answers out of Vexen, Axel shows up and hits him with his chakram. Axel explains to Vexen that he needs to eliminate him before he tells Sora the truth. He says that death is preferable to being a Nobody, yet despite that, Vexen still begs for his life. His pleading turns out to be all for naught as Axel snaps his fingers and engulfs the Chilly Academic in flames, making Vexen the first Organization member to die. Sora asks Axel what kind of being he is, but even he doesn't know. Axel vanishes, having dealt with his mission.
Axel returns to where Larxene and Marluxia are waiting for him. It is revealed that Marluxia is also part of the coup to overthrow the Organization's leader. Larxene explains that killing Vexen was actually a loyalty test for him to join the traitors, to prove that he has what it takes to turn on another Organization member. Larxene and Marluxia decide that it's finally time for Naminé to meet Sora, but they warn her not to betray Sora's memories. Marluxia tells her to manipulate his memories to lead him closer to her before disappearing along with Larxene.
Downstairs, Sora reunites with Riku. Sora expects Riku to be back to normal now that Vexen is dead, but to his surprise, he's still insistent on preventing Sora from meeting Naminé. Riku says he made a promise to keep Naminé safe, much to Sora's surprise. As Riku goes on to explain the story behind the promise, it turns out to be the exact same as Sora's story. Both boys insist that they're the one who made the promise to her. Sora pulls out his good luck charm to prove it, confusing Riku. Suddenly, Riku's forehead flashes, and he pulls out an identical charm, claiming that Sora's is a fake. The two fight, and Sora wins yet again. After the fight, Riku runs away, dropping the good luck charm on the way out. When Sora picks it up, it turns into another World Card, this time representing Sora and Riku's home world of Destiny Islands.
Sora wants to continue, but Donald and Goofy stop him, trying to figure out why Sora and Riku have the exact same memories. Sora starts to think they're trying to say that Riku is right and he is wrong, but they explain they're just concerned. They can tell something is wrong, but Sora is blinded by his memories. They try to explain why they're concerned, but due to his obsession with Naminé, Sora gets angry and yells at them. They try to reason with Sora, but he ignores them and runs ahead. Meanwhile, Axel, who is alone with Naminé, tells her that he won't stop her if she tries to leave. She thanks him and runs away. Left alone, Axel hopes Sora will make things interesting. He's enjoying himself so much that he laughs, much to his surprise. Before Sora enters Destiny Islands, Jiminy tries to call him out for snapping at Donald and Goofy, but he yells at Jiminy too. He turns to the door and proceeds, with nothing on his mind except for Naminé...
