Sora expects to return to the Mysterious Tower after closing the final Sleeping Keyhole, but instead he ends up in the World That Never Was, the headquarters of Organization XIII. He assumes that he must be in the real world since he closed all the Sleeping Keyholes, but he is still in his younger body. Suddenly, Xigbar appears. He tells Sora that he and his allies have been leading him along the entire time. Sora recalls seeing the robed figure on Destiny Islands, the Mysterious Figure in various worlds, and Xemnas in Prankster's Paradise and the Grid. Xigbar reveals that the robed figure he met at the beginning of his first journey was only there to give them an entry point into Sora's dreams. Sora expresses his disbelief that they could have been planning that far ahead, and even Xigbar admits that the plan is too perfect.
Xigbar points out that Sora is still wearing the clothes he had on for the Mark of Mastery, meaning that he's still in his dreams. He shoots twelve bullets around Sora, and these twelve bullets reveal twelve hooded figures, including the Mysterious Figure, who takes Sora to a vision of the past on Destiny Islands. The Mysterious Figure reveals that he is actually a younger version of Master Xehanort himself, and the Robed Figure, whom he had met in the vision, was actually Ansem SoD before he possessed Riku. Apprentice Xehanort gave up his body and became a Heartless so that he could time travel, just like Sora. In his bodiless form, Ansem went to the past to meet his younger self and explain his plans to him. Young Xehanort takes Sora to just before Destiny Islands was destroyed, where he sees himself entering the secret cave after Ansem. Next, they go to Traverse Town, where Sora sees all the past versions of himself representing the many times he had been to that world.
After that, Sora finds himself back at the World That Never Was, where he finds that he has returned to his older body. He encounters Naminé, who tries to run away. Sora tries to stop her so he can finally thank her, but when he does, she transforms into Xion, whom Sora does not recognize. To his surprise, Sora finds himself crying, but Xion runs away after putting her hood up. Sora hears a faint voice of Riku telling him to wake up, but he is too confused to listen to it. Further ahead, he meets the hooded figure, but this time it has transformed into Roxas. He reminds Sora that it could've easily been the other way around; if Roxas had won his duel with Sora, he would have taken his body. Now, though, Roxas realizes that only Sora can save everyone. Roxas grabs Sora's hands, causing him to see his Nobody's memories. Roxas disappears, leaving Sora seemingly alone and back in his young body again. Riku calls out to him again, but Sora continues to ignore his voice.
Later, Sora seemingly reunites with Riku and Kairi, but when he catches up to them, they turn into Aqua and Terra. They call him "Ven," and unbeknownst to Sora himself, his own body transformed into Ven's. Terra and Aqua leave, and Sora returns to his older body. He tries to follow them, but he can barely move. Riku calls out to him again, but to no avail. A bright light appears, and Sora finds himself back on Destiny Islands, where he sees himself and Riku as little kids. He recalls the time Aqua met them, but he suddenly sees a vision of Ansem, who sends him flying out of the illusion.
Back in the World That Never Was, Sora encounters Xigbar again. He tells Sora that everything he just saw was a dream, but that they were the ones who put him to sleep. Sora realizes that there's no way someone like Roxas couldn't have a heart, since his illusions allowed him to feel what he did. Xemnas appears and explains that Nobodies can in fact grow new hearts. Xigbar reveals to him that Organization XIII's true goal was actually to fill all its members with Xehanort's heart, turning them all into vessels for Xehanort. When Sora asks him how he could stand to become another person, Xigbar further reveals that he himself was already half-Xehanort, as demonstrated by his golden eye. Xemnas says that most of the original Organization members were not ideal candidates to become Xehanort vessels, which is why the first Organization failed. Sora becomes furious that the Organization would abuse the heart like that. Xigbar tries to entice him to joining them, but he refuses, citing the connection with his friends as the source of all his power. Xigbar begins to panic after seeing Sora's strength, so he leaves Xemnas to deal with him.
Sora and Xemnas have a lengthy battle, with Sora emerging victorious. Xemnas seemingly fades away again, but Sora collapses due to exhaustion. Young Xehanort returns and tells Sora that the "X" on his chest was actually a symbol called the Recusant's Sigil, which gives the Organization a means of tracking him. He reveals the reason behind their sending him into slumber: they plan to turn Sora into the final vessel. By sinking him into the deepest darkness of sleep, the Organization plans to fill Sora with Xehanort's heart. Once he falls asleep, Young Xehanort takes Sora's body to the Organization's meeting room, Where Nothing Gathers, as he awaits the arrival of the other members. Within his heart, Sora is nearly lost to darkness, but Ventus, who is still within him, encases him inside his Keyblade Armor. The armor is corrupted by the darkness, but Sora's heart is kept safe and sound. Now lost in the folds of sleep, all Sora can do is count on Riku to rescue him...
