The DLC begins from the final scene in Olympus, starting where Xigbar (who as the Post-Credits Scene reveal is actually the Lost Master, Luxu) says, “May your heart be your guiding key”, while watching Maleficent and Pete take their leave to search for the Black Box elsewhere. He gets a surprise visit from Luxord, who proposes a riddle about a wild goose chase that Xigbar shrugs off and insists he stick to his mission to find the Black Box. Luxord instead questions Xigbar about the mission he was given, namely why the box is so important if no one knows the contents, and who was it that gave the order: Master Xehanort or Xemnas? Luxord notes it can't be Xehanort, because he only cares about the Keyblade War and starting the upcoming clash between light and darkness, so it's rather odd for him to show interest in something completely unrelated to his goal. Therefore, the order had to have come from either Xemnas - the main administrator of the Seekers of Darkness - or Xigbar, the one who passed the order to Luxord. Though Xigbar insists Xemnas gave the order, Luxord reveals he personally asked Xemnas only for the Nobodies’s leader to not know what he was talking about. Caught, Xigbar denies knowing what’s inside the box, claiming that he heard during his travels that it holds secrets vital to all Keyblade Wielders. Luxord sees through it, especially when Xigbar weakly claims hearsay, and suspects that Xigbar's true reason for ordering its search is because someone else is trying to find it, and Xigbar wants to keep its connection to him a secret. Even though Xigbar refuses to answer his question about his identity, Luxord shrugs it off and smugly decides to feign ignorance before leaving to continue his search for the box, leaving Xigbar fuming and nettled at someone figuring him out.
- Xigbar: The question is, who are you, Luxord?
In the present, Sora resolves to find the missing Kairi after Master Xehanort’s defeat. In a flashback, a discussion takes place between the younger Xehanort and the Master of Masters, who had let the former try out the darkness-shielding black coat during his tour throughout the worlds. Xehanort tells the Master how he had seen many people with darkness hidden behind a false light within their hearts, claiming that they act like good people while secretly desiring great power under the belief that their reasons are justified to maintain a sense of self, causing their darkness to grow. Xehanort admits he understands this desire for power, but still wants to do something about it before the growing darkness brings chaos to the worlds, stating that he somehow has the feeling he knows what to do (due to having traveled to the future and letting the experience ingrain itself into his heart despite having no memories). The Master encourages him to follow his heart instead of letting the upcoming Mark of Mastery exam tell him the answer, promising him he can control the darkness and gain great power once he does so to the point he will no longer need the black coat. When Xehanort asks for the Master’s identity, the Master warns him that he could lie about what it is by making numerous claims about it, while telling Xehanort a person's actions speak better than their words. But when Xehanort persists, the Master tells him his name (which is not heard by the player) and reveals himself to be a Lost Master before taking his leave, much to Xehanort’s shock.
- The Master of Masters: May your heart be your guiding key.
Seventy-five years later, sometime after the events of Dream Drop Distance, Master Xehanort meets with Xigbar and Saïx in the Keyblade Graveyard. Master Xehanort briefly reflects on his meeting with the Master of Masters, but soon moves on to discuss the current members of the new Organization XIII. Saïx reports that Marluxia, Larxene, and Luxord are currently out on their missions (Locating the New Seven Hearts for the former two and finding the Black Box for the latter). When Saïx questions Luxord’s mission, Xigbar talks his way out of it, and a bemused Master Xehanort shrugs it off, wanting to continue discussing the vessels.
Saïx confirms that the hearts of Ansem, Xemnas, Riku Replica, Vanitas, and Young Xehanort have returned to their proper places in time, and that Vexen and Demyx are planned to be brought in as back-ups. Xigbar believes the Seekers are short a twelfth vessel, but Master Xehanort explains that he had already placed the heart of Terra-Xehanort into the body of Terra (which had been restored following the destruction of Ansem and Xemnas, but because Terra's heart couldn't return to his body, Master Xehanort was able to claim it easily). As he explains, one can only disappear completely if their heart and body is complete, which is one of the reasons why he divided his heart into vessels. Xigbar asks what’s the plan for the thirteenth vessel, and Saïx says the plan is that once Vexen returns, they will have him refine the replicas they were using to anchor the time-displaced hearts of Ansem, Xemnas, Young Xehanort, Vanitas, and Riku Replica after they were sent back to their time.
Saïx reveals that Vexen created 20 replicas during his time as a member of the Organization, the first twelve becoming mindless puppets because they're too unstable to be vessels (these are the very same replicas Sora, Donald, and Goofy would fight in Scala ad Caelum), the next two replicas became Riku Replica and No. i (Xion before she was given a name; it’s revealed that even though she disappeared from everyone’s memories, records of her still existed in Vexen's research), and the next five becoming vessels for Ansem, Xemnas, Vanitas, Young Xehanort, and Riku Replica. Saïx suggests they have the heart of No. i inhabit the last replica and make her their thirteenth member due to her connection to Sora, a proposition Master Xehanort accepts. Saïx leaves to go and recruit Vexen while Xigbar departs to continue his mission, leaving Master Xehanort to repeat the Master of Masters's last words to him from their conversation.
- Master Xehanort: May your heart be your guiding key.
Sora makes it back to the Final World and meets Chirithy again, explaining the situation to him. Chirithy tells Sora that the Power of Waking is meant to awaken and restore sleeping hearts rather than restore hearts that have been completely erased from existence; since Sora already used it six times to awaken the other Guardians’ hearts, he altered the course of history and broke a nature taboo. He warns him that if he goes through this again, he will pay a heavy price: not only will Sora lose his powers, including the Power of Waking, he will vanish from the world and be unable to return without his powers. Undeterred, Sora still insists on going through with his journey to save Kairi. Chirithy instructs him to return to the time when Terra-Xehanort attacked them all and go through the hearts of the Seven Guardians of Light until he reaches Kairi’s heart, helping them in their struggles along the way and using the connection formed to save her.
- Chirithy: That's all the advice I can give you. Beyond that, I can only say, may your heart....be your guiding key.
Sora enters the heart of Ventus after he is knocked down by Terra-Xehanort, hearing a mysterious voice (which is inaudible to the player) calling itself "Darkness" and criticising Ven for being 'too pure' and 'careless'. When Sora questions if the voice is Vanitas, the voice instead manifests as/summons the Dark Inferno χ Heartless and attacks/sics it on him. Upon defeating the Heartless, Sora enters the heart of Aqua, experiencing the sadness and fear she felt during her time trapped in the Realm of Darkness, which caused her to hallucinate Anti-Aqua among the Demon Tide and give up the fight. Sora fights the embodiment of this trauma in the form of Anti-Aqua and is victorious. Upon reaching the tear in the fabric of space-time leading to the new timeline, Sora meets Naminé in his Station of Awakening. Naminé informs him that she contacted Terra’s thoughts in the form of the Lingering Will and told him about the situation the Guardians are in, allowing him to come to the rescue in the new timeline. However, the Lingering Will intends to destroy Terra-Xehanort in order to save Aqua and Ven and is too blind with rage to listen to Naminé. Sora has Naminé go back to the Final World so she can return to Kairi's heart, while he goes to prevent Terra from destroying himself. Sora saves the Lingering Will from Terra-Xehanort after the latter has his Guardian, the Dark Figure, restrain it. However, Sora soon ends up caught in the Dark Figure's grip and the Lingering Will intercepts Terra-Xehanort’s attack, sacrificing itself to save Sora. Enraged, Sora clashes with Terra-Xehanort, a battle which ends in the latter restraining him with the Dark Figure before launching a wave of darkness at him.
Sora soon finds himself in the body of his past self back in the Skein of Severance, fighting against the members of the Real Organization XIII once again. Here, the player has the chance to play as Riku, Aqua, and Roxas in their battles, with each battle having a new scene from their perspectives:
- After defeating Xigbar and Dark Riku, Riku stays in the area long enough to meet Demyx, who was send by Ienzo to pick up another replica vessel for Naminé's sake. Although wary of Demyx, Riku does allow him to take Dark Riku's former vessel, all the while asking him to be careful with it not only because it will be a vessel for Naminé, but also because it holds important memories of Riku Replica.
- Just after making it to Terra-Xehanort and Vanitas' position in the labyrinth, Aqua and Ventus speak with Terra-Xehanort and Vanitas. Ven vows to free Terra from Xehanort’s possession and tries to get Vanitas to come home into his heart, since he believes that Vanitas being a part of him means they are 'one and the same'. Vanitas rebukes this however, stating he was always an individual being within Ventus and Xehanort simply tore him out, with neither Ven nor Aqua caring to get more information before fighting the two Seekers of Darkness. After the battle is over and Terra is restored to his body, Sora realizes Terra had protected him when Xehanort enveloped him in darkness.
- After making it to Saïx and No. i's position in the labyrinth, Kairi and Lea speak with Xemnas and Saïx about their newest member, where they reveal No. i's nature as one of their experimental replicas, and how they were able to recreate her from Vexen's records and Young Xehanort's experiments into creating a heart, despite not remembering her. Lea attacks No. i to find out who she is and is completely caught off guard when she summons a Keyblade identical to Sora's. When Lea questions if No. i is Roxas, Saïx rebukes this (while also subtly jogging No. i's memories by saying the names of her closest friends, Axel and Roxas), and Kairi confirms Saïx's words when she sees a girl's face under the hood. Once Sora arrives to help and Roxas calls out No. i's name, Xion, through Sora's mouth, the latter witnesses her memories leave his heart to return to her. Sora would then speak with Roxas just before he leaves his heart to enter his new body, requesting Sora's aid in reclaiming something that connected his heart with his friends from Xemnas. Sora and Kairi help the trio get the drop on Xemnas before he incapacitates and drains the former two of their energy, forcing Sora's heart to leave his past self and enter Roxas to aid him in the battle against the Xemnas and Saïx. Roxas, Xion, and Lea are able to land a simultaneous blow on Xemnas, reclaiming the Recusant's Sigil that represented the bond they formed during their time as members of the Organization. While the mark will disappear with Xemnas, Roxas wanted to reclaim it for himself and his friends. Once Roxas finishes his speech, Xemnas proceeds to abduct the weakened Kairi, and the battle against Saïx plays out just like it did before.
After Sora, Riku, and Mickey defeat Ansem, Xemnas, and Young Xehanort, Sora is forced to witness Master Xehanort strike down Kairi in front of him once again. Mickey telepathically contacts Sora and explains that Xehanort crystallized Kairi to keep her as insurance until he opened Kingdom Hearts, and there is still a chance to save her. Sora realizes he can search for her by following Master Xehanort into Scala ad Caelum ahead of his past self. There, Sora finds five pieces of Kairi’s heart scattered across the town (with the last one being held by a Darkside Heartless) before he is confronted by Master Xehanort, who reveals there are only two pieces left and taunts Sora for being almost out of time to save her, forcing Sora to enter his past self during his battle against Xehanort’s replicas. While the past Sora, Donald, and Goofy battle against Master Xehanort himself, Sora realizes he can find the last two pieces by tracing his heart’s connection to the last two Guardians, Riku and Micky.
Meanwhile, back in the Keyblade Graveyard, the Keyblade wielders holding back Kingdom Hearts are suddenly attacked by Xehanort's Replicas (who had been released by Master Xehanort after Sora's party destroyed his armor), now each one carrying a copy of his No Name Keyblade. Riku, Terra, Ventus, Roxas, Lea, Mickey, Aqua, and Xion hold off the replicas long enough for Sora to arrive and claim the sixth piece from his connection to Riku. However, the replicas soon turn the tides of battle and scatter everyone through the Keyhole portals, with Mickey being the only one left. Entering Mickey, Sora helps him fend off and take out the Replica Xehanorts, using their connection to find the final piece. Now that he has all seven pieces, Sora connects the hearts of the Guardians of Light and is finally able to restore Kairi. Confronted by a copy of Armored Xehanort, formed from all the replicas fusing together, Sora and Kairi team up to defeat their opponent (the player even has the option to play as Kairi). The two help the other Guardians of Light reunite, and with their combined power, destroy Armored Xehanort. They then help the Guardians reach the past Sora’s location just after he has defeated Master Xehanort with the help of Donald and Goofy. Reuniting in the Final World, Sora and Kairi invite Chirithy to come home with them. Sora spends his last moments with Kairi, going to Disney Castle to see the fireworks, reunite Chirithy with Ventus at the Land of Departure, watch the sunset at Twilight Town while eating sea salt ice cream, and finally go to Radiant Garden to place Naminé’s heart within her replica body. The ending, post-credits scene, and secret ending play out just as it did before.
