A long time ago, just after the Keyblade War in the Keyblade Graveyard, the blue moon of Kingdom Hearts shone. While it does, the Foreteller Luxu watches from afar...
In the Mysterious Tower, Yen Sid is talking to Riku, Kairi, and Mickey. He tells them that the time has come to rescue Ventus, Terra, and Aqua so they can join the Guardians of Light. Yen Sid explains that Ven was put in a secure place, but only Aqua knows where he is, so they have to rescue her first. This prompts Mickey to tell them the story of how he met her in the Realm of Darkness once.
Aqua's story picks up where it left off at the end of Birth By Sleep's Secret Episode, with her finding the Castle of Dreams in the Realm of Darkness. When Aqua approaches the castle, she is attacked by some Heartless. As she fights them, she wonders how much time has passed in the Realm of Light, since time does not flow in the Realm of Darkness. She tries to approach the castle, but the path crumbles in front of her, forcing her to take another path. She finds herself in a village, where more Heartless appear. After defeating them, she reminisces about her life before she fell into the Realm of Darkness. She realizes that the inhabitants of the Castle of Dreams were lost to darkness just like her.
After Aqua reaches the bridge to the castle, it collapses as the castle's clock goes haywire. She realizes that because there is no true time in the Realm of Darkness, she can manipulate the clock to restore the bridge. After finding all the gears to restore it, she tries to return to the castle, only to be attacked by an amalgamation of Shadows called a Demon Tower. Aqua destroys it and enters the castle. Inside, she sees an illusion of Terra. She tries to talk to it, but it doesn't respond. After the illusion disappears, Aqua realizes that if the Castle of Dreams is empty, perhaps its inhabitants are still alive.
Next Aqua reaches the ruins of the Dwarf Woodlands. She sees Snow White's casket, but it has an illusion of Ventus in it. Seeing the illusion reminds her that she promised to wake him up, which she laments that she hasn't been able to do. She turns around and sees a mirror. When she touches it, her reflection grabs her and pulls her inside, where she finds herself in a castle. Aqua searches for some other mirrors in the castle, but they pull her inside. In the mirror world, a phantom of herself appears. After defeating the phantoms, Aqua realizes that they were the personification of her own self-doubt, showing that her despair has grown due to being in the Realm of Darkness for so long.
Aqua then comes upon the remains of Enchanted Dominion, where she sees illusions of both Ven and Terra. She follows them through a forest of thorns until she encounters a Darkside. She manages to destroy it, but it is only one of many Darksides. After fighting through them all, she sees the illusions of Terra and Ven again. This time, Terra speaks, but he doesn't see Ven. He tells Aqua that he is just there because her heart is showing her what she wants to see. The reason he can speak to her is because his heart is connected to the darkness. Terra tells Aqua that Xehanort is looking for Ven. Aqua looks over at Ven and turns her back to Terra. As she does, Xehanort takes control of him. He gets Aqua to reveal that Ven is in the Chamber of Waking, but Terra begins to fight back. While Terra fights with Xehanort, a Darkside grabs Aqua and Ven. Aqua goes unconscious as Terra attempts to chain Xehanort within himself.
The unconscious Aqua drops her Wayfinder, but Mickey grabs it and wakes her up. Before they can talk, another Demon Tower appears. Mickey tells her that the black monsters are called Heartless, and the two of them battle the Demon Tower. They manage to injure it and force it to flee, but they don't destroy it. When Aqua asks, Mickey tells her that it's been ten years in the Realm of Light. She tells him what happened since the battle in the Keyblade Graveyard, and he tells her about the Heartless attacking worlds. Mickey explains that he is looking for the Kingdom Key D, the counterpart to Sora's Kingdom Key needed to close the Door to Darkness, which must be closed from both sides. He gives Aqua the Wayfinder back, and she realizes that it led Mickey back to her. Mickey says the old phrase "May your heart be your guiding key," which was once used by Keyblade wielders in the ancient past.
Aqua and Mickey arrive at the ruined Destiny Islands, which Aqua recalls. She tells Mickey about how she met the young Sora and Riku, and Mickey tells her that they are the ones who are helping him. They go to the secret cave of Destiny Islands, but they are attacked by a larger version of a Demon Tower called a Demon Tide. After defeating it, they see the door inside the cave, the door that once contained Destiny Islands' Keyhole. Inside, they find the Kingdom Key D, which Mickey takes. With that key, they can close the Door to Darkness.
Aqua and Mickey find themselves at the Door to Darkness. Mickey tells her that it's the door to "Kingdom Hearts," but not the true Kingdom Hearts. Riku arrives to help them shut the door, but another Demon Tide emerges and goes after him. Aqua tries to stop it, but it manages to break free. The Demon Tide attacks both her and Mickey, tearing the latter's shirt off. It takes Aqua back through the door to Destiny Islands, which then disappears. She is forced to fight this Demon Tide on her own, but after talking to Terra and Mickey, she has regained the will to keep fighting, knowing that she will return to the Realm of Light someday. Mickey is saddened that he was separated from her, but he has to continue his mission, so he goes to help Sora close the door. After Ansem is defeated and the Door to Darkness is closed, the worlds consumed by darkness begin to be restored. Aqua rests on the beach, laying her Keyblade beside her on the shore. She watches as Destiny Islands fades away and returns to the Realm of Light. Aqua accepts her fate and falls back into the darkness. As she does, the Keyblade gets separated from her because she wasn't holding it when she fell back into darkness, which will eventually result in it appearing on Destiny Islands. We then get a brief glimpse of her approaching Ansem the Wise later, after Kingdom Hearts II.
Back in the present, Mickey finishes telling his story. Riku gets angry that Mickey never told him about Aqua's sacrifice, wishing that he could have helped her. Yen Sid reveals that he told Mickey not to tell Riku so that he or Sora wouldn't do anything reckless and try to go save her when he wasn't ready. Now, though, the time is right, and Mickey and Riku are ready to return to the Realm of Darkness to look for Aqua. Kairi asks Yen Sid what she can do, but he says that she still needs to train first. When she learns that she'll be training with Lea, she is initially horrified due to his kidnapping her before, but Mickey assures her that he has changed. Yen Sid gives Riku and Mickey new clothes from the Good Fairies that will shield them from the darkness, and the two of them take their leave to find Aqua.
A bit later, Sora returns to the Mysterious Tower after having played with the Dream Eaters in Traverse Town. He, along with Donald and Goofy, go to the top of the tower, but Sora is shocked to see no one else is there besides Yen Sid. The elderly Master tells Sora that he needs to train because he was severely weakened after nearly becoming Xehanort's vessel. He further says that Chip and Dale are analyzing the data Ansem the Wise gave to Riku in Sora's heart in the hopes that it can help them find their missing friends.
Yen Sid tells Sora that he needs to learn the Power of Waking since he failed to learn it last time. He suggests that Sora go visit Hercules, since he went through a similar experience of losing most of his power. Sora, Donald, and Goofy head out to the Gummi Ship to travel to Olympus, but they can't figure out how to navigate the ship since the old gates are closed. Goofy recalls the phrase "May your heart be your guiding key," which Sora repeats. Hearing this phrase reminds Sora of the strength of his heart, which he uses to open a path to Olympus. With that, the three friends are ready to begin their next adventure to save their friends and settle things with Xehanort once and for all.
