Sora, Donald, and Goofy can finally return to Twilight Town after a long time of fruitless searching for Riku and Mickey. As soon as they arrive, Vivi runs up to them, telling them that Seifer is in trouble. They head to the Sandlot, where they find the gang under attack by some Nobodies. After destroying them, they are greeted by a member of Organization XIII, specifically Number VII. He warns Sora that Axel has betrayed the Organization, and that he is now planning to turn Sora into a Heartless. He says that the Organization doesn't want Sora to get hurt, but Sora doubts the sincerity of his words. The Organization member removes his hood, revealing him to be a blue-haired man with golden eyes named Saïx. He tells Sora that the even if Nobodies don't have hearts, they know how to injure them. He urges Sora to keep fighting the Heartless before hinting that he knows Riku's whereabouts. Sora tries to follow him as he leaves through a corridor of darkness, but it closes before he can reach it.
After Saïx leaves, Seifer thanks Sora for fending off the Nobodies by giving him the Struggle trophy — the real one. Pence comes up to him and tells him that he and his friends found Kairi, asking them to come to the train station. Before leaving, they find another Absent Silhouette, this time of Lexaeus. After defeating it, they return to their mission and make their way to the station. When they arrive, they are met by Hayner and Olette, who tell them the story. Axel showed up at their "usual spot" abducted her. Hayner and Pence tried to attack him, but to no avail; he took her back into the corridor of darkness, followed by Pluto, before it closed.
Sora gets very angry after hearing that Kairi got kidnapped. He startles Goofy, who was holding the trophy, causing him to drop it. The four multicolored orbs fall off, and Hayner, Pence, and Olette each pick one up, with Sora grabbing the blue one. Sora holds it up to the glowing sun, just like Roxas did. Goofy pulls out the pouch he got from Mickey the last time they were there and pulls out the orb that Ansem took from Roxas in the simulation. The orb that Sora is holding begins to glow and reveals the gate to the next world. Sora unlocks it and bids farewell to his friends. He promises to return, and with that, they take their leave.
Back at the Organization's headquarters, Saïx reports to the Superior. It turns out that Saïx had been given orders to tell Sora that he needs to keep fighting the Heartless. The Superior explains that he wanted Saïx to deliver this message to make Sora doubt himself; if he knows that Organization XIII wants him to fight the Heartless, he may be hesitant to do so, but that hesitation will make him angry, ultimately fueling his desire to keep going. Saïx asks the Superior about Axel, and he says that the only thing they should feel for him is pity. With Sora now unsure about his mission, he continues onward, though with uncertainty in his heart...
