After returning to the real world, Sora, Donald, and Goofy tell Leon the new password, which is their own names. He leaves to go check on the town while Sora accesses the computer. He tries to search for information on Riku and Kairi, but it gives him an error message. Goofy tries to ask the computer about the Nobodies and Organization XIII, but those searches also yield errors. Sora starts smashing random keys in frustration until a picture of an unknown man with blond hair and orange eyes pops up.
Mickey enters the room and congratulates them on completing their mission. Mickey sees the picture of the blond man and identifies him as Ansem the Wise, much to the trio's confusion. Sora drags Mickey back into the lab and directs him to the picture of the silver-haired man. He tries to remind Mickey that this man, the one they fought in their previous journey, was actually Ansem, but Mickey realizes he didn't finish telling them the important information he tried to explain previously. Finally, Mickey reveals the big secret about their old adversary: he wasn't actually Ansem at all, but merely an impostor. The silver-haired man stole Ansem's name and identity, even writing reports under his name, until he unleashed the Heartless on Hollow Bastion. The false Ansem eventually turned himself into a Heartless, and that Heartless was the man they defeated on their first journey.
Sora and friends are completely taken aback from the revelation. They can't believe they went through all that work just to defeat a fake, but Mickey reminds them that fake or not, he still was a huge threat to the worlds, so he had to be stopped. Goofy asks Mickey that if the false Ansem, who called himself the "Seeker of Darkness," then what happened to the real Ansem, who was known as "the Wise?" Mickey explains that finding the real Ansem was one of his main goals, and that was why he wanted to access his computer so badly.
Goofy realizes that, if the fake Ansem became a Heartless, then he must have also created a Nobody. Mickey reveals that not only does he have a Nobody, but his Nobody is actually the Superior, the leader of Organization XIII; in other words, their entire journey has been dedicated to fighting two halves of the same man. Mickey says that he remembers meeting the false Ansem, and he looked really similar to the Superior, but unfortunately he can't remember where or when he met the impostor. He says that if they find Ansem the Wise, then he could tell them the identity of his impersonator. Sora tries to ask Mickey where Riku is, and he seems to know something, but he refuses to answer. He tells Mickey that the Organization kidnapped Kairi. Mickey says that they should look for their friends before trying to find Ansem the Wise.
Suddenly, an earthquake shakes the castle, so they rush outside to see what's going on. A huge army of Heartless, led by Maleficent and Pete, is doing battle with the Nobodies, but it is becoming apparent that the Heartless are losing. Pete flees in fear, but Maleficent stubbornly refuses to surrender. The Nobodies continue to gain the upper hand, but when Sora and friends show up, Maleficent orders the Heartless to attack them instead. The trio fights a mixed group of both Heartless and Nobodies and manages to emerge victorious. Maleficent flees, and when the three fairies Yuna, Rikku, and Paine show up and find out where she is, they are very disappointed. They begin to think that they chose the wrong side. Donald lies and tells them that Leon has lots of treasure, so they go to help him out.
The trio runs outside, fending off Nobodies, until they are stopped by a beam of light. From that light emerges Sephiroth, Cloud's archenemy. Sora tells him that Cloud was looking to settle the score with him, so Sephiroth goes to find him. After he disappears, they notice a hole in the castle wall, but they decide to ignore it for now. They find Leon and Aerith fighting some Heartless and Nobodies, so they help fend them off. Further on, they see a massive army of Heartless advancing toward the town. Everyone is fighting the horde of foes: Yuffie, Aerith, Stitch, Yuna, Paine, Rikku, Leon, Cloud, and even Sephiroth. The latter clears the Heartless away to get to Cloud. He urges Cloud to give in to the darkness before vanishing. Tifa appears and nearly catches up to Cloud, but he flees because he doesn't want to confront his past. The Heartless surround Tifa, but they are no match for her. Before Sora and friends can advance further, Mickey tries to stop them, telling them to go find Riku and Kairi instead. Donald and Goofy trick Mickey so they can continue to help. Mickey isn't disappointed, as he realizes that they are following their hearts.
While the fierce battle is raging outside, something else is happening in the castle. A hooded figure, a member of Organization XIII, enters Ansem's lab. A security system spots him, but he destroys it before inserting a disc into the computer. He enters a different password, the names of Ansem's former apprentices, before being granted access to a hidden part of the castle. He walks down a very long flight of stairs into a hallway. As he does, he recalls the time he once spent in the castle: he was one of Ansem the Wise's apprentices. He asked his master for permission to perform an experiment involving Hollow Bastion's Keyhole and the heart of the world, but Ansem forbade it. In his memory, Ansem referred to him by his true name: Xehanort. At the end of the long hallway, the mysterious figure finds a circular room. He sits in a chair in this room and looks at something on the ground: a blue suit of armor with a Keyblade beside it. As the figure speaks, his voice is revealed to be that of the Superior, the Organization's leader, thus revealing that Xehanort was the name of the man who stole Ansem's identity. Xehanort's Nobody looks at the suit of armor and refers to it as his "friend."
We then see a flashback, around or slightly before the time of Sora's first adventure, when Organization XIII was still incomplete and the members from Castle Oblivion were still alive. Zexion is walking through the Organization's headquarters when he is stopped by Vexen. Vexen asks him where the Superior is, referring to him by his true Nobody name: Xemnas, which is an anagram of "Ansem," the name that Xehanort stole, with an "X" added onto it. Zexion informs Vexen that Xemnas is in a place called the Chamber of Repose, much to his chagrin. Vexen storms off, but Zexion is stopped again, this time by the Organization's Number II, who is still wearing his hood. Zexion reminds Number II that he and Xaldin were supposed to be out recruiting new members, but he says that he already found one, namely Marluxia. Zexion tries to leave, but Number II stops him, trying to ask him about the Chamber of Repose. He explains that there was once a fearsome battle between Keyblade warriors, which Xehanort was involved in. The battle caused Xehanort to lose his memories, and he was taken in by Ansem the Wise as his apprentice, until he betrayed his master. The Chamber of Repose was designed for studying darkness, but Ansem the Wise ordered it to be sealed off. When Xehanort got rid of Ansem the Wise, he immediately reopened the Chamber of Repose. Now Xemnas goes off and talks to someone in that chamber every now and then. Zexion says that the Organization needs to focus on finishing work on Castle Oblivion. Number II tells Zexion that there's a counterpart to the Chamber of Repose called the Chamber of Waking. He says that the real reason Xemnas sent the Organization into Castle Oblivion was to find the Chamber of Waking, where his other "friend" is.
Back outside, Sora and friends are met by Demyx, who again seems reluctant to fight them. After they insult him for not having a heart, he says that Nobodies actually do have hearts, but they don't believe him. Demyx refers to Sora as a "traitor" and attacks. They fight him once again, but this time they manage to destroy him. Demyx screams as he fades away into oblivion. After the battle, Mickey confronts them, but he says that he approves of them going to help Leon and the others. Up above them, a battle between a Heartless and Nobody sends a rock flying in Mickey's direction. Goofy pushes him out of the way and gets hit in the head, knocking him down. Sora, Donald, and Mickey think that he died, which makes them furious. Mickey removes his Organization cloak and charges ahead, with Sora and Donald close behind him.
The three of them fight their way further through the canyon, helping their friends on the way. They reach a cave, where Goofy shows up, explaining that he was just knocked unconscious. They make their way to the bottom of the canyon, where they see the Superior appear on top of a cliff. He takes off his hood to reveal his face, which looks very similar to both Xehanort and his Heartless, "Ansem." Seeing his face jogs Mickey's memory, and he remembers meeting Ansem the Wise. During the meeting, Xehanort, still an apprentice of Ansem's at the time, barged in to ask about the experiment he was performing, but Ansem, who was more concerned about the worlds, forbade it. Mickey recalls Xehanort's name, much to the amusement of his Nobody. They try to go after him, but they are stopped by the army of Heartless.
Sora finds himself in a fierce battle against a huge army of 1,000 Heartless. It is a long and arduous fight, but he ultimately manages to destroy them all. When they go to confront the Superior, Mickey calls him by his original name of Xehanort, but he says that he hasn't gone by that name for a very long time. Sora asks him where Riku and Kairi are. He says that he doesn't know where Kairi is, but he tells Sora to ask Mickey about Riku's whereabouts before vanishing. Axel appears and tells them that the Superior's name is Xemnas. He explains that having Sora destroy the Heartless is all part of Organization's plan; every time Sora destroys a Heartless with the Keyblade, the captive heart is freed. The Organization's plan requires the use of those hearts, which they have been collecting.
Sora tries to ask Axel about Kairi, but Saïx appears, forcing him to flee. Sora tries to stop Axel from escaping, but Saïx stops him, ensuring him that they'll punish Axel. Saïx explains that the Organization took Kairi and that they are detaining her in their headquarters. He tells Sora to beg to let him see Kairi, which he does, but he doesn't let Sora see her. Sora becomes furious, but Saïx tells him to direct his rage at the Heartless. He says that the hearts that Sora has been freeing will come together and form Kingdom Hearts, at which point they can become whole again.
Maleficent appears and says that she will take Kingdom Hearts for herself. She summons Heartless to attack Saïx, but he summons some Dusks which easily dispose of them. The Dusks prepare to attack the trio, but Maleficent forms a barrier around them, and the Nobodies attack her instead. She assures Sora that this doesn't mean that they're allies now; she just wants to use him to eliminate Organization XIII. She tells him to leave and find a way to defeat them, but he refuses to leave while Saïx is still around. The Dusks manage to overcome Maleficent, and Saïx proceeds to replace them with Heartless. He explains that Heartless simply follow whoever is the strongest; since the Organization defeated Maleficent, they now serve them instead. Sora defeats a few Heartless, but when their hearts are released, Saïx smiles. He urges Sora to keep collecting hearts before disappearing. The hearts Sora just freed are wrapped in a cloak of darkness before they vanish. Sora refuses to fight anymore, and he begins to fall into despair, realizing that he's been helping Organization XIII the whole time. Suddenly, a light envelopes the trio and warps them away.
Meanwhile, the Organization is having another meeting. Saïx wonders if it will be harder to control Sora now that he knows that defeating Heartless helps their plan, but Number II assures him that Sora's inherent desire to help people will ensure that he will keep fighting. Number II wonders if it would be a bad idea to kill Sora, since eliminating him would seemingly ruin their plan. Xemnas says that if Sora were weak enough to be defeated by one of them, then he would be useless anyway, so they are free to fight him as they wish. These words are pleasing to Xaldin, who seems eager to fight Sora soon.
Back in the Gummi Ship, Sora recalls how they escaped. Maleficent sent them through a portal of darkness, after which they found themselves in a black void. In the void, a hooded figure wearing the Organization's cloak left them a box before disappearing. The box contained a picture from the digital Twilight Town: it included a picture of Roxas, whose name Sora was able to recall despite having never met him before. There was also some ice cream in the box, which served as the next gate. Sora unlocked it, and after doing so, they found themselves back in the ship. Sora says that he feels that Riku was the one who gave the box to him. Sora asks what they should do if they encounter more Heartless, since defeating them would help Organization XIII's plan. Goofy says that they really have no choice but to fight. Now unsure about what to do, the trio can only return to the worlds they visited previously in order to find a path to the Organization's headquarters...
