The end is finally at hand. Sora, Donald, Goofy, and Mickey step through the portal and find themselves in the World That Never Was, Organization XIII's stronghold. As they look up into the sky, they see skyscrapers towering over them in a dark city. Suddenly, two Samurai Nobodies appear and separate Sora from Donald and Goofy. A portal of darkness appears behind Sora, and a hooded member of Organization XIII appears behind him. He summons a Keyblade and attacks Sora. Suddenly, Sora finds himself inside his own heart, fighting the Organization member, who now wields two Keyblades. Though Sora doesn't know it, the two Keyblades, Oathkeeper and Oblivion, identify him as Roxas. He tells Sora that he fought Riku and won before asking him why Axel chose to help him instead of bringing him back. Roxas nearly wins the duel by separating Sora from his Keyblade, but Sora summons it back to him, giving him the chance to deliver a finishing blow.
In a flashback, we see the birth of Roxas, right after Sora became a Heartless. Sora's Nobody appeared in Twilight Town, and the first person to approach him was Xemnas. He offered to give Sora's Nobody a purpose by letting him join the Organization. Having just been created, he didn't know anything else, so he accepted. Xemnas rearranged the letters in Sora's name and added an "X," creating the name "Roxas." Within their hearts, Axel and Roxas reunite one last time. Axel tells him that the time is approaching for him to rejoin Sora. He finds himself wondering if what Xemnas said about Nobodies not having hearts is true. Axel asks Roxas what he thinks, but he isn't sure, and he says that Sora will find the answer one day. They reminisce about the day they met before Roxas leaves. Back in Sora's heart, Roxas's hood falls down, and he accepts his fate. Back outside, Donald and Goofy tell Sora that they didn't see Roxas; they just fought the Samurai.
Just as the group reaches the edge of the city, Saïx approaches Kairi in her cell, taunting her over her being used for their plans. After he leaves, Naminé appears behind her and opens a portal to help her escape. Their hands meeting causes a bright light to shine, which Sora sees from far away. He uses the Keyblade to open a path into the castle. Meanwhile, Naminé is beginning to fade away. As Kairi's Nobody, touching her caused her to begin being reabsorbed into Kairi. Saïx tries to stop them, but a figure appears behind them, a hooded figure with the Soul Eater. Naminé refers to him as Riku, and he destroys the Berserker Nobodies surrounding Saïx. He tries to fight Saïx himself, but he escapes by opening a corridor of darkness. Before he can pursue Saïx, Kairi stops him. She pulls down his hood, but it's not Riku she sees underneath; the hooded figure is revealed to have the face of "Ansem" Seeker of Darkness/Xehanort's Heartless.
While venturing through the castle, Saïx confronts Sora and friends. He tells them that the Organization's goal is almost complete, directing them to the heart-shaped moon in the sky, which he calls Kingdom Hearts. Saïx says that they only need a few more hearts, so he summons a horde of Heartless. Kairi calls out to Sora from the balcony a few floors up. She tries to jump down to reach him, but she is stopped by some Heartless on her floor. She is rescued by Riku/Ansem, who gives her a Keyblade of her very own. As if things weren't bad enough for the Organization, Maleficent and Pete show up too! Maleficent plots to take their castle for herself, but Pete has his doubts that she can succeed.
Meanwhile, higher up, Mickey fights his way through some Nobodies until he finds none other than DiZ, whom he saves from some Dusks. DiZ removes the wraps concealing his face, revealing him to be the real Ansem the Wise. He tells Mickey that he was trying to stop the Organization to get revenge on his traitorous apprentices, especially Xehanort. Ansem the Wise tells Mickey about Riku's fight with Roxas; he assumes that Riku lost the fight, forcing him to rely on the powers of darkness, which transformed him into Ansem SoD/Xehanort's Heartless. Mickey tells him that Riku was so ashamed of himself that he made Mickey promise not to reveal the truth to Sora.
Back downstairs, Sora shakes off the Heartless, but he gets confused when he sees Kairi fighting alongside "Ansem." The remaining Heartless are destroyed by Xigbar, who refers to Sora as Roxas. Xigbar insults Sora's skill with the Keyblade, saying that he pales in comparison to the Keyblade wielders of the past. Xigbar jumps down to greet Sora, and they fight. Sora and friends emerge victorious, but Xigbar refuses to tell him anything about Roxas. He fades away, leaving the Organization with only three members: Xemnas, Saïx, and Luxord.
At the top of the castle sits a place called the Altar of Naught, where the Organization offers hearts to Kingdom Hearts. Xemnas stands upon the altar, urging Kingdom Hearts to share its power with the Nobodies. Saïx appears and asks him if they've collected enough hearts. Xemnas says that now it's only a matter of time before Kingdom Hearts is complete. Since they don't need any more hearts, Saïx is free to dispose of Sora, much to his delight.
Sora and Kairi finally reunite and share a hug. As "Ansem" is about to leave, Sora stops him. He says that despite all the horrible things he did, he's grateful for him saving Kairi, meaning he can't be all bad. "Ansem" tries to leave, but Kairi stops him and tells Sora that he is actually Riku, much to his shock. He is overcome with joy to be reunited with his friend, but he can't understand why he didn't reveal himself. Riku says that he still needs the power of darkness until the Organization is destroyed, so he has to stay in the form of Ansem SoD/Xehanort's Heartless.
Meanwhile, near the top of the castle, Ansem the Wise is setting up a machine that will turn the Organization's Kingdom Hearts into data, foiling their plans and giving him a new research opportunity. Before the heroes can go farther, Luxord stops them and separates Sora from his friends. Luxord plays a deadly game with Sora, but he manages to win the game. Luxord calls out to Roxas as he fades away, leaving only Saïx and Xemnas left in the Organization.
Sora and his friends confront Saïx and finally battle him. Saïx, who has kept up the front of a cold stoic up until now, finally has permission to show his true feelings of anger and rage. He goes Berserk, revealing himself to be a maniac on the inside. Saïx tries to draw upon the power of the moon to fuel his anger, but even that is not enough, and he is defeated. As Saïx fades away, he laments the fact that he was never able to obtain a heart. With him gone, Xemnas, the Superior and the one behind everything, is the only member of the Organization left remaining.
When Sora asks Riku about Roxas, he finally provides an answer, telling him that Roxas was in fact his Nobody, which is why he had the power to use a Keyblade. He explains that Roxas betrayed Organization XIII and fought himself. Riku wasn't strong enough to defeat Roxas on his own, so he had to remove his blindfold, transforming him into Ansem SoD/Xehanort's Heartless. With the power of Ansem's Guardian, he was able to subdue Roxas, but it brought great shame to Riku. Shortly after, Ansem the Wise in his DiZ disguise appeared. When Riku tried to tell him that Roxas felt a connection to Sora, DiZ told him that Nobodies can't feel anything.
Higher up, Ansem the Wise begins laughing, calling himself a fool for thinking he could encode hearts. He tells Mickey that the simulations in his virtual Twilight Town ended up developing hearts of their own, causing them to act in unexpected ways. The machine begins to overheat, and Ansem tells Mickey that it's about to explode, which could cause anything to happen. When Sora and friends arrive, Ansem apologizes to Roxas for the way he mistreated him. Xemnas appears and sees all his adversaries ready to end his schemes. He blames Ansem for creating the Heartless, since Ansem's research is what encouraged him (as Xehanort) to take things farther. Xemnas tells him that he is going to use the power of Kingdom Hearts to create a new, perfect world, but Ansem says that any world ruled by Xehanort would be an "empire of ignorance." Ansem's machine explodes, and Riku shields his friends from its blast, which seemingly kills Ansem.
Though Ansem did not succeed in encoding Kingdom Hearts, his machine did expel the hearts from the massive moon. As the hearts fall into the city, the Nobodies desperately try to grab them, but to no avail. Darkness envelops the hearts, turning them back into Heartless; in other words, many of the Heartless defeated up to that point have been reborn. The explosion of the machine somehow transformed Riku back into his true self. At Sora's insistence, he removes his blindfold, which he had previously used to contain Ansem SoD within him. Now, though, the explosion purged Xehanort's Heartless, allowing him to take it off. They look up to see that some of the hearts are being reabsorbed into Kingdom Hearts, while others have become Heartless again. Now their last mission is to defeat Xemnas. Riku takes off his Organization cloak, and together they head for the top of the castle.
Before reaching the top, the horde of Heartless begins to catch up to them. Before they can fight off the Heartless, Maleficent and Pete appear to hold them off while the heroes go to fight Xemnas. Maleficent assures them that once he has been defeated, they will take the castle and try to plunge the worlds into darkness again. Sora tries to stop them, but Mickey says that they are following their hearts, so they should let them do it.
The heroes finally reach the Altar of Naught, where Xemnas urges them to go recollect the hearts for him. When they refuse, Xemnas tries to sow seeds of doubt within them by making them sympathize with his cause, asking them why they fear darkness and why they hate him. Though he acts sad, Sora doesn't fall for his manipulation and shuts him up. An amused Xemnas admits that his words were merely an attempt at manipulation, since he can't feel any emotions. He transports himself and Sora to the huge skyscraper back in the city, the same skyscraper where Riku fought Roxas, for a one-on-one duel, where Xemnas's fighting style reveals him to be the unknown figure Sora had fought a year ago back in Hollow Bastion. He uses the same moves as last time, but Sora has gotten much stronger since then, so he emerges victorious with ease. Still, though, Xemnas seems to have been letting him win; as Sora delivers the final blow, he says "So, it wasn't a fallacy..."
After seemingly defeating Xemnas, Sora returns to the Altar of Naught. Xemnas reappears and calls upon the power of Kingdom Hearts, absorbing its energy to make him stronger. A door appears, which Mickey says was created by the worlds. After some preparation, they head through the door, where they see Xemnas standing on top of a distant building. Sora, Donald, Goofy, and Riku are separated from the others, and they charge towards the fortress ahead of them. At the top of the fortress, they see Xemnas wearing a massive suit of armor. They seemingly defeat him and are returned to the Altar of Naught once more. Xemnas calls out to the hearts' power of anger and rage, but Sora tells him that hearts have all kinds of emotions, not just hate. When Sora asks him if he can remember, Xemnas says he can't before seemingly fading away.
Sora asks Riku if he's going to come back to Destiny Islands. He seems hesitant to do so, but Sora encourages him. The castle begins to collapse, so Riku tries to open a corridor of darkness, but to no avail; after shedding the Organization's cloak, he no longer has the power to create them. Naminé appears and creates a corridor, but only Sora and Kairi can see her. Roxas emerges from Sora, and the two of them finally get to reunite. They say that as long as Sora and Kairi are with each other, they will be together as well. With that, Roxas and Naminé go back into Sora and Kairi. Everyone begins to leave, but before Sora and Riku can enter the corridor of darkness, it closes.
In the distance, Sora and Riku see Xemnas's fortress transform into a monstrous dragon. They take a nearby hoverboard and use it to injure the dragon, revealing that Xemnas, once again in his suit of armor, is still alive in its head. As they prepare to face him, Sora realizes that he forgot to thank Naminé like his journal said, but Riku assures him that he can do it when they get home. They defeat the armored Xemnas, but the battle is not yet over. They find themselves in a white void, where Xemnas has his final showdown with the two of them. He proclaims that nothingness will exist for eternity before attacking. After a ferocious final battle, Xemnas is finally destroyed. With that, both Xehanort's Nobody and Heartless have been destroyed, and Organization XIII with them.
Sora and Riku don't have any time to rest, unfortunately, as a huge army of Dusks appears to get revenge for their Superior. Much like Axel, Riku puts an immense amount of energy into a single attack, but he manages to survive. The Dusks are destroyed, leaving them free to try and escape the void. They manage to leave it, but they find themselves on a beach, known as the Dark Margin, in the Realm of Darkness. Sora and Riku decide to accept their fate and live together in the Realm of Darkness, but suddenly a bottle washes up on the shore. Sora opens it to find the message Kairi sent him before. It reads:
"Thinking of you, wherever you are.
We pray for our sorrows to end, and hope that our hearts will blend.
Now I will step forward to realize this wish.
And who knows: starting a new journey may not be so hard, or maybe it's already begun.
There are many worlds, but they share the same sky, one sky, one destiny."
After reading the message, Sora and Riku suddenly see a door of light open in front of them. It is the Door to Light, the counterpart of the Door to Darkness they shut at the end of their first adventure. They step through the light and find themselves back in Destiny Islands. At long last, after everything that has happened since the night of the storm, the three friends are finally reunited and back home. Their other friends Donald, Goofy, and Mickey are there as well. As Sora and Kairi look at each other, they see reflections of Roxas and Naminé inside them. Some time later, Sora and Riku are relaxing on the beach when Kairi brings them a letter from Mickey. As they open the letter, they learn that their quest is not yet over, thus leading into the next chapter of their journey.
Eleven years prior, three armored figures meet at a crossroads in a field of abandoned Keyblades. After pulling out Sora, Riku, and Mickey's Keyblades, they see an elderly man approaching...
The lost two
Memory of Xehanort
Chasers
Keyblade War
It all began with...
birth by sleep.
- Boss Rush: Luxord and Sa'ix are fought in quick succession from a hub level.
- Characters Dropping Like Flies: Axel, Xigbar, Luxord, Sa'ix and Di Z all bite the dust.
- Evil Counterpart: Dark City is a nighttime city much like Traverse Town of the first game, and while it does have a nice cyberpunk film-noir Gotham aesthetic to look at, the place is utterly lifeless and hollow and swarming with heartless.
- I Don't Like the Sound of That Place: The levels are named such things as; 'The Brink of Despair', 'Hall of Empty Melodies', 'Altar of Naught'.
- Weird Moon: There is a heart-shaped moon in the sky hovering over the castle and city.
