Sora and his friends, Riku and Kairi, plan to leave Destiny Islands to explore the other worlds when one day Sora meets a strange hooded man inside the secret cave. The man tells Sora he came to see the door that leads to other worlds. After a stranger conversation, Sora goes back to his house and falls asleep. He gets woken up by a storm and rushes outside to save the raft but instead sees a huge black hole in the sky and monsters start appearing around him. Sora finds Riku before they get engulfed in darkness. A Keyblade appears in Sora’s hands and the darkness disappears, but Riku is nowhere to be found. Sora runs to the door to find Kairi standing in front of it. A gush of wind flies Kairi through Sora and he finds himself back on the beach with the Island destroyed. After fighting against a huge monster, Sora finds himself in a strange town.
Meanwhile, Donald finds a letter from King Mickey letting him know that something bad is happening and he has to go check into it. Mickey asks Donald and Goofy to go to Traverse Town and talk to Leon about the person that has the “key”. With Queen Minnie’s approval, Donald and Goofy leave for Traverse Town.
In Traverse Town, Sora finds himself battling against some guy that wants to take the Keyblade away from him because he thinks Sora isn’t worthy of it and gets knocked out. After waking up, Yuffie and Leon explain to Sora what the Keyblade is and that the creatures, the Hearltess, were after his heart. In the other room, Aerith is explaining the same thing to Goofy and Donald with the addition of mentioning Ansem’s report. They suddenly get attacked by Heartless and that’s when Donald and Goofy meet Sora. After they agree to stick together, we see shadows of the villains around a table arguing about how to deal with Sora.
The trio visit Wonderland first. After landing, they see a white rabbit that keeps repeating he’s late. They try to follow him, but come across a tiny door. Drinking the potion to get smaller, they cross the door and arrive in the middle of Alice’s trial where she is accused of trying to steal the Red Queen’s heart. Sora wants to help her, but Donald says they’re not supposed to meddle. Hearing what she is accused of, Sora ignores Donald and tells the Red Queen he knows Alice didn’t do it and he can prove it. After finding proof that it wasn’t Alice the culprit, the Red Queen still doesn’t listen and Alice ends up inside a cage. Sora fights off the card guards and thinks he delivers Alice, but when he opened the curtain, Alice wasn’t in the cage anymore. He tries to find her and ends up face to face with a monster. After fighting it, the door wakes up and a light shines inside its mouth/keyhole. Sora’s Keyblade immediately reacts and a beam of light goes inside the hole. We then see the villains worry that Sora has found one of the Keyholes but Maleficent reassures them that he has many more to go and he still doesn’t know their plan with the princesses. As she says that, we see Alice appear in the same room as the villains.