Back at Hollow Bastion, Pete informs Maleficent that none of the Disney villains she worked with before are interested in rejoining her council. Maleficent asks Pete to tell her about everything that has happened while she was dead. Later, in Disney Castle, Chip and Dale inform Minnie that there are lots of thorns in a place called the Hall of the Cornerstone. Just then, Sora, Donald, and Goofy happen to be arriving at the castle as well. Chip and Dale greet the trio and urge them to get to the library. They fight their way through the hallways, defeating Heartless as they go along.
At the library, Minnie asks for their help, and the group splits up. Donald and Goofy go to warn everyone else in the castle while Sora escorts the queen to the throne room, fending off Heartless as he does. The throne room has a magical seal which Minnie undoes. Much to her horror, the throne room is full of Heartless as well. Minnie manages to open up a secret passage underneath the throne, causing a huge light to appear and destroy all the Heartless in the room.
Minnie explains that beneath the throne room is the Hall of the Cornerstone, which contains a sacred object called the Cornerstone of Light. It has the power to repel darkness, meaning that Heartless usually are incapable of getting in. Donald and Goofy arrive, having finished their mission, to see the Hall of the Cornerstone full of thorns. Maleficent creates a projection of herself, finally revealing to them that she was resurrected. She tells them that she intends to take the castle for herself, but she must fill it with darkness first, which is why she decided to corrupt the Cornerstone of Light.
The trio decides to seek Merlin's help. They return to Hollow Bastion and inform him about the problem, and he teleports them back to the Hall of the Cornerstone. After investigating, he creates a door, which he explains will lead them to another world where they can find the one responsible for polluting the castle with darkness. He tells them that there should also be an identical door somewhere in that world, which the enemy is using, so he tells Sora to close it. He gives them a warning to resist temptation to do "something dark" while they're there, and with that, they head inside.
The trio finds themselves in a black-and-white world called Timeless River, where the Cornerstone of Light rests. They encounter Pete and chase him down to a dock. When he hears a steamboat whistle, Pete attempts to leave, but Sora and the gang stop him. They defeat him with ease, but they soon start to realize he isn't the Pete they're looking for. He tells them to find his stolen steamboat if they want to apologize, so they agree. After returning to the hill, they see several windows which lead to strange locations with Heartless (and some fire) in them. In each area, they see Mickey trying to deal with a problem, so they help him out. Every time they do, they see a flashback from someone's perspective.
In the first flashback, they see Maleficent chastising someone for trying to replace her while she was gone. He tries to object, but she says he won't be able to enjoy a taste of power when she takes over. In the second, he cries and wishes he could go back in time, causing a bright flash of light behind him. He turns around and finds a Timeless River door. Next, he is seen showing Maleficent the door. She gives him one more chance to prove himself to her. In the final flashback, Maleficent gives him his objective: destroy the Cornerstone of Light. They finally realize that these flashbacks are from Pete's perspective. He resolves to steal his old steamboat from his past self before carrying out his mission.
The gang spots the present-day Pete, who has already taken the Cornerstone of Light. They head down to the river, where past Pete tries to stop his present self but fails. Present Pete takes the Cornerstone on the steamboat while trying to attack the trio from afar. They manage to destroy the cage around the Cornerstone, and they proceed to chase present Pete. They find him in a fight with his past self, who helps them defeat present Pete. He summons the door and escapes, but Sora manages to close the door like Merlin asked. Past Pete thanks them for helping by letting them pilot the steamboat. Donald tries to change the past, but Sora and Goofy drag him back into the present, remembering what Merlin said about temptations.
Back in the present, Minnie, Merlin, Chip, and Dale watch as the thorns vanish. Sora gets to meet Daisy for the first time, and the Cornerstone of Light turns out to be the portal to the next world. He opens the gate, and the trio heads out for their next destination.
Much later, near the end of their journey, Sora and friends return to Disney Castle, where they find a strange portal waiting for them. On the other side, they find themselves in a mysterious world they've never seen before. They find what appears to be a golden suit of armor, but when they approach, it begins speaking to Sora. It seems that the armor has the mind of someone trapped inside of it. The armor, known as the Lingering Will, can sense that Sora has a Keyblade, and it assumes him to be Xehanort because of this. The Lingering Will attacks, and the three friends battle it. After an intense fight, the Lingering Will realizes that it was wrong in assuming Sora to be Xehanort. It goes back to sleep, waiting for the real Xehanort, vowing to get revenge on him one day...
