In a seemingly endless realm where the sea meets the sky, a translucent Sora wakes up, wondering where he is. After exploring the void for a short time, he is met by none other than Chirithy, who explains that he has entered the Final World, which is a limbo between life and death. The nothingness of death exists beyond this plane of existence, and this is where people who have died but still have someone in the land of the living holding onto them end up. Chirity reveals that Sora has briefly visited this realm before during his visits to the Station of Awakening, since sleep and death sometimes touch and allow for cross-overs. Chirithy also confirms that Kairi's light is the only thing keeping Sora from death, and that if he wants to leave, he must conceptually put himself back together.
Sora begins collecting numerous avatars of himself wandering around the Final World, and slowly but surely, his body begins to regenerate. During his mission, he counters stars, the lingering spirits of other people in the Final World. Some are children hopelessly trying to find their parents; others are people separated from their loved ones.
One such star is Namine, who ended up here after Kairi fell to the Demon Storm. Sora insists that he will bring Kairi and the others back, and vows to thank Namine in person (claiming that his earlier thanks in the datascape didn't count). Namine reveals she's been in contact with Terra, whose lingering will still persists, and that she'll reach out to him again and see if he can help turn the tides.
Another star has no name, and reveals to Sora that she was killed by surprise when she was still alive. The one person she knows who is holding on to her and keeping her in the Final World is someone that Sora appears to know, but she won't say who, other than it's someone who has lost their identity and has replaced it with someone else's identity. Sora promises to find the person and tell them.
At last, Sora is reformed, and asks the question of who is keeping Chirithy here in the Final World. Chirithy insists they don't work like that, and that their former friend is probably happier with their new friends anyway. When implored, Chirithy suggests that Sora use the Power of Waking to try to revive his friends.
Soon, Sora finds himself back where he fell at the Keyblade Graveyard, only this time, he is transported to the Dive to the Heart once again. He is then taken to an apparition of Olympus, where suddenly, Jiminy pops out from his hood, having survived the ordeal at the Keyblade Graveyard. Sora proceeds to find Riku's hovering spectral form suddenly being accosted by the Lich, a unique Heartless that takes Riku's Heart from his body. Sora and Jiminy pursue the Lich and beat Riku's heart out from him. Riku's heart returns to his body, and Jiminy explains that he will return to the Keyblade Graveyard where he died.
Sora subsequently does the same for Donald, Goofy, Mickey, Ven, Aqua, and Lea, journeying to the various worlds he's been through and fighting off the Lich for their hearts and lives. However, in the apparition of San Fransokyo, Young Xehanort appears and warns Sora that there's a high price for abusing the Power of Waking...
His mission complete, Sora finds himself in a black void, but is met by Kairi there. Overjoyed to reunite with her, Sora tells Kairi he feels strong with her, and Kairi simply insists that all she did was believe he'd be safe. They join hands as they return to the land of the living and reunite with the other Guardians. Time has been reset to just before their previous defeat, and feeling reinvigorated by their return from beyond the veil, the Nine Guardians of Light press on to the Keyblade Graveyard.