The Guardians of Light are once again confronted by Terra-Xehanort, but this time, before he can strike Ven down, he is stopped in his tracks by none other than Terra's Lingering Will. The phantom relishes finally having his chance for vengeance after over a decade of waiting, and with his spectacular Keyblade transformations and abilities he quickly begins to overpower Terra-Xehanort. The battle soon turns into a flurry of Keyblade strikes that takes their duel away from the clearing. However, the Guardians of Light are soon besieged by yet another monstrous horde of Heartless, Nobodies and Unversed. Sora, Donald, and Goofy defeat a Demon Tide, but it soon sucks in every enemy creature present to once again form the Demon Storm. This time, Sora is undeterred, and charges it alone...
... and in a white void, Sora encounters Ephemer, who offers his help. All around the Keyblade Graveyard, the Keyblades of the fallen union members of ancient times rally around Sora in a massive current. Sora rides the army of Keyblades and together, they are able to vanquish the mighty Demon Storm.
The Guardians express awe at the light of the past returning to help them, but they are confronted by the Dark Riku. Mickey believes that this Riku is the Ansem-possessed Riku who battled Sora during his first visit to Hollow Bastion, but it doesn't matter, as Dark Riku summons a shadowy specter of Master Xehanort and another swarm of enemies. Xigbar appears and challenges the Guardians to prove they have what it takes to face the Thirteen after their previous defeat. The two leave, and the Guardians are quickly pinned down by the sheer numbers of the enemy. Things grow desperate; Aqua and Ven try to volunteer for a suicidal diversion to let the others through, and Mickey nearly wastes his energy on a massive Time spell before Riku talks him out of it. As the horde closes in, things look bleak... until a mighty light strikes the area and sends the enemies flying.
The group looks up and see that none other than Yen Sid has arrived on the battlefield to rescue them. With two hands, Yen Sid parts the sea of enemies with ease, and orders the heroes to go on to face Xehanort while he holds the horde. Donald and Goofy decide to stay to back up Yen Sid, and assure Sora he can handle himself - he's a whole pint by himself. The Seven Guardians of Light race through the corridor of light conjured by Yen Sid, ready to face their destiny.
Sometime later, the Guardians arrive at the crossroads of the Keyblade Graveyard. All is quiet, until finally, the moment arrives.
On the horizon, the Thirteen Seekers of Darkness arrive, flanking Master Xehanort himself. The Thirteen meet the Seven at the center of the crossroads, and all twenty pieces of the χ-blade face each other at last as it was ordained all those years ago.
- Master Xehanort: Today, we join these other wielders and leave our mark on fate. I have waited patiently, but together, we will unlock the Keyblade War's secrets. Now, we forge it: the ultimate key - the χ-blade!
Master Xehanort brandishes the ancient No Name Keyblade and plunges it into the ground, giving rise to a massive labyrinth, the Skein of Severance. As the Seven Guardians of Light and Thirteen Seekers of Darkness engage each other, Master Xehanort watches from atop a colossal pillar as the Second Keyblade War finally begins.
At this point the player has to choose between two boss battles in two rounds of fighting (the first round being Dark Riku and Xigbar, or Luxord, Marluxia and Larxene; the second round being Saix or Terra-Xehanort and Vanitas). Individual fights will be retold in chronological order, but the order the rounds are listed here are not in a set chronological order.
Sora finds Riku struggling to keep Dark Riku and Xigbar, who are being overseen by Ansem, at bay. Shortly after Sora joins the fight, Ansem takes his leave, and Sora and Riku battle Dark Riku and Xigbar. When Xigbar is felled, he laments that he would've fared better with a Keyblade, and when Sora and Riku scoff he's unworthy of one, Xigbar protests that he is worthy. Xigbar explains that he only ever joined Xehanort out of the master's promise to bequeath his to him, and teleports to the top of the labyrinth, where he backs up until he falls to his presumed death, to Sora and Riku's horror.
Dark Riku is defeated and protests that he's the real Riku as he begins fading away. However, the Riku Replica emerges from Riku and explains that Dark Riku isn't a time-traveling Riku; he's just another Replica. Riku Replica purges Dark Riku from the Replica, leaving it blank for Namine to inhabit. As Riku realizes what must be done, Riku Replica calmly accepts his fate and passes on with Dark Riku.
While Riku goes after Ansem, Sora comes to the aid of Mickey, but the King of Disney Castle is showing little effort fending off a combined assault from Marluxia, Larxene, Luxord, and even Xemnas all at once. Xemnas oversees the fight from outside the battlefield until he gives Luxord an extra boost of dark power before departing the scene. Luxord traps Mickey in a card and challenges Sora to one final game of finding him amongst his cards - while Marluxia and Larxene continue to attack Sora the whole while.
Luxord is swiftly defeated and praises Sora for being so good at his games. He gives Sora a "wild card" which he says could help turn the tables somehow. Sora smiles at invites him to play again after Luxord is recompleted, and the Organization member happily accepts and looks forward to it.
Mickey is freed from Luxord's card and rejoins the fight. When Larxene is defeated, she bemoans that she lost to Sora's group yet again, but admits it's better than serving as one of Master Xehanort's vessels. Sora asks why then, did she join the Thirteen, and Larxene playfully says she was just along for the ride with someone - her secret, before she fades away. Marluxia is defeated, and begins genuinely laughing as his memories of his past life begin flooding back to him. As he fades, he expresses gratitude to Sora for helping him reclaim his identity.
Mickey goes after Xemnas, and Sora proceeds past a maze of shifting walls as he goes deeper into the labyrinth. He comes upon Kairi and Lea facing off with Saix and a hooded girl. Though Kairi and Lea are struggling thanks to being new to the Keyblade, Sora briefly manages to turn things in their favor before Saix enters his Berserker mode and overwhelms them all.
Xemnas arrives and lambastes Lea for his defection to the Guardians of Light, musing that he once trusted him to deal with turncoats himself. However, Lea defiantly refuses to back down and attacks Xemnas, who casually grabs and destroys Lea's Flame Liberator Keyblade. After torturing him with his lasers as Saix watches on passively, Xemnas prepares to slay Lea for all the trouble he's caused him, and moves to strike him with one of his blades... only to find the hooded girl holding him back.
Xemnas mockingly asks if she's changing sides again, and disagrees with her attempt to convince him to spare Lea, until he orders her to take his life. Sora steps in and begs the girl to not go through with it, which sends the girl into a tearful rage as she attacks him. Sora tries to get her to stop, and using a familiar voice, says her name - "Xion". Xemnas interrupts and kicks down Xion, removing her hood in the process. However, before Xemnas can do any more, a light erupts from Sora's chest, flies off, and then returns with an almighty blast into the labyrinth. As Xemnas watches in shock, a hooded dual-wielding Keyblade wielder emerges from the dust - Roxas.
Roxas explains to Xemnas that with the help of Ansem the Wise, Ienzo, and others, he was able to return in a new Replica body once Sora provided the connection needed to restore him to life. Roxas mocks Xemnas's supposed mastery of manipulation since some of the hands involved in his return are in league with him right now. Xemnas furiously goes for Kairi, kidnapping her and departing to spite Sora. While Lea takes a rest, Sora engages Saix with Roxas and Xion, but quickly finds he can only contribute a limited amount of support since Roxas and Xion are all too eager to repay the Organization's former lieutenant for all the misery he caused them.
When Saix falls, Lea curses him for letting Xehanort reduce him to a glorified attack dog, and they finally have it out. Saix was jealous when Lea found new friends in Roxas and Xion, feeling he'd forgotten him and their quest to find the mysterious girl at Radiant Garden. The two are able to make peace as Saix fades away. Sora moves on, while Roxas, Xion, and Lea are left behind. Xion begins crying as she meekly approaches her two long-lost best friends, and Lea jokes that he should've brought some ice cream before he and Roxas, too, are reduced to tears. The trio shares a long-overdue embrace.
Sora goes on to find Aqua and Ven facing off with their decade-old rivals, Terra-Xehanort and Vanitas. Sora and Ven are able to defeat Vanitas and crack his visor, and Sora is shocked to find that Vanitas's face matches his own. Ven laments that he and Vanitas were never allowed to choose between light and dark thanks to their sifting, but Vanitas scoffs at this, since he did choose to join the side of darkness. Sora questions why he won't stand by their side, but Vanitas calmly explains that he does stand by their side as the shadow they cast. Though Sora is repulsed, Ven grimly accepts when Vanitas professes that he is and always will be of darkness.
Terra-Xehanort is brought down, but when Aqua and Ven try to awaken Terra within him, the young form of Xehanort reasserts itself and begins tearing Sora, Aqua, and Ven asunder with dark chains representing their bonds. Terra-Xehanort prepares to kill Aqua and Ven by dropping them from a huge height, and Ven can only weakly cry that he kept his promise to Terra. As Terra-Xehanort lets go, Aqua and Ven plummet...
Only for The Person Behind You, Xehanort's Guardian Heartless, to quickly zoom in and rescue Aqua and Ven, and gently leave them on the ground. Terra-Xehanort screams that this isn't possible, but the dark entity has none of it and quickly subdues him before ripping the bandages from its mouth. Soon, the entity begins speaking... in Terra's voice, reciting his decade-old vow to make things right and protect his friends. The truth comes out - The Person Behind You has in fact been the container for Terra's heart all along. Sora comes to Terra's aid and helps him purge Xehanort from his human body once and for all. Terra tearfully reunites with Aqua, thanking her for always lighting his way back, and thanking Ven for keeping his promise. Sora moves on, and the Wayfinder trio remain behind to recuperate.
From this point on, standard chronological order returns barring the order that the enemies are defeated.
Sora scales the Tower of Endings, the final stepping stone to where Master Xehanort has been observing the events of the Keyblade War. He meets Riku and Mickey, and they are quickly confronted by the lions of the Thirteen Seekers of Darkness: Xemnas, Xehanort's Nobody who laid the groundwork for the Thirteen with his Organization; Ansem, Xehanort's Heartless who abandoned his body to travel back in time to engineer the decades-long scheme and later gathered the Princesses of Heart; and Young Xehanort, who was tasked by Ansem with gathering the Seekers from across time and space all those years ago. From on high, Master Xehanort reveals that the defeats of nine of his Seekers of Darkness have yielded nine extra copies of No Name, and that four more are needed to forge the χ-blade. After Sora questions Xemnas about Kairi's whereabouts, he realizes that Xehanort has kidnapped her specifically to motivate them into participating in these final clashes, even though it will play directly into their enemy's plans. Riku steps forward, and despite acknowledging that Master Xehanort is well within reach of his goal of summoning Kingdom Hearts, they will defeat him once again. Master Xehanort admits it's possible... if they survive that long.
Keyblades, magic, and the magic of both dark and light furiously clash in this penultimate showdown between Sora, Riku, Mickey, Xemnas, Ansem, and Young Xehanort. The three lieutenants are occasionally assisted by Master Xehanort, who summons swarms of Keyblade Graveyard debris to isolate Sora so that his henchmen can attack him as a unit. Despite their best efforts and despite having once been world-ending threats in their own right, the three Xehanort's find themselves no match for the heroes who have become stronger and more powerful in all the years they have suffered from their torment.
When Xemnas falls, Sora demands to know what his heart is feeling, and if it was really worth it all. Alas, the former leader of Organization XIII admits that it wasn't, and that he regrets treating his companions like nothing, because they are now all gone and have left him with nothing. When Xemnas mournfully declares that the loneliness and pain of a heart is all there is to having one, Sora refuses and says it's part of being human. Xemnas gives him one last grimace, and admits that being human must take incredible strength as he dies.
Upon Ansem's defeat, he muses on the long journey he and Riku have had. The young Keyblade Master admits in some sort of way he's going to miss him, but Ansem affirms that he has become stronger than darkness. Ansem admits that he realized a long time ago that he would never succeed, but this realization and the betrayals of the Organization broke him, and he went along with it out of seeing no other way out. Ansem uses his last breath to encourage Sora and Riku to move on from all of this, and to go and seek new things in their lives.
When Young Xehanort is defeated, he simply cackles as he doubles over in pain. When Sora demands to know what he's laughing at, Young Xehanort once again claims that Sora is due to pay a severe price for overusing the Power of Waking. Young Xehanort doesn't have any cathartic moment as he fades, since he will simply go back to his time and live out the rest of his life and see it to fruition right now... but Sora's time is up, he ominously warns as he fades.
His last, best followers defeated, Master Xehanort is unperturbed, and collects three more copies of No Name, leaving him with just one to go. He begins the ritual to summon Kingdom Hearts and invites Sora to face him one last time... but not before he provides him motivation. As Sora watches in horror, Master Xehanort brings forth Kairi's body and slays her, with her destruction producing the thirteenth and final key. Sora, Riku, and Mickey are unable to stop Xehanort, even when Mickey tries to use the mighty Ultima spell, which is countered by Xehanort's powerful Stopza. At last, the χ-blade is complete, and Master Xehanort ascends into the sky and corrupts the moon of Kingdom Hearts, ready for the apocalypse to begin at last as darkness rains on the Keyblade Graveyard.
A crying Sora is comforted by Donald and Goofy, and Terra, Aqua, Ven, Roxas, Lea, and Xion arrive on the scene as well. As they wonder what to do, Mickey and Riku are freed from Xehanort's Time spell and know what to do. Master Xehanort's abuse of time travel has turned him into a living time machine, which they can use against him to contain him somewhere else while they contain the spread of the corrupted Kingdom Hearts. Though Mickey initially asks Keyblade Masters Riku and Aqua to help him, Sora refuses and volunteers to defeat Master Xehanort while the others contain Kingdom Hearts, aided by Donald and Goofy. Everyone agrees. Before Sora can set out, Xion approaches Sora, and tells him that she can feel that Kairi will be okay.
While the others use their Keyblades to attack Kingdom Hearts, Sora, Donald, and Goofy forcibly open a portal to somewhere unknown through which they take Master Xehanort with them, ready to end it once and for all...