On board the Gummi ship, Sora receives a call from Chip and Dale, who explains that Riku and Mickey are in trouble at the Realm of Darkness. In panic, Sora and company are forced to go there in order to save their friends. However, Chip and Dale remind them that Mickey's Keyblade is a Keyblade from the Realm of Darkness and thus allows him to easily enter the realm; Sora and company do not have such a Keyblade.
Thinking quickly, Sora decides to use his heart as his guiding key and sets off to Destiny Islands, where he finds the Master's Defender, a long-abandoned Keyblade, on the shores. On Goofy's suggestion to use it as another guiding key, Sora uses the Master's Defender, unlocking the door to the Secret Place as a door to the Realm of Darkness. Donald and Goofy want to join Sora, but Sora tells them that he has to do it himself, and goes through the door alone.
Meanwhile in the Dark World, Riku and Mickey are overwhelmed by another Demon Tower, which this time incapacitates Mickey and disarms him of his Keyblade. As Mickey is trapped in a dark orb, the shadows surrounding the tower disperse into another figure, which picks up his Keyblade and muses on how familiar it is. The figure decloaks from the darkness, revealing themselves to be...
The newly corrupted Anti-Aqua accuses Mickey of abandoning her in the Realm of Darkness for over a decade, describing how she had to fight to survive even after losing her Keyblade. She declares that now, Mickey and Riku will have to share the misery and rage in her heart. However, Riku's own heart is contacted by his replica, now wielding a repaired Way to the Dawn and offering him his strength. As Riku retaliates, Anti-Aqua orders the Demon Tower to attack.
The Demon Tower's strength nearly overwhelms Riku once more, and he whispers Sora's name. Just then, the door from the Secret Place opens, revealing Sora. The two friends combine forces and once again perform the Mirage Split and Nightmare's End Reality Shift, summoning a massive Keyblade and cleaving the Demon Tower in two. Anti-Aqua charges at Riku, but Sora blocks the blow, ordering Riku to keep Mickey safe while keeping her at bay.
Eventually, Sora defeats Aqua, purging the darkness from her. She falls into the waters, wondering if this is the end, but Sora reaches his hand, allowing her to pull free. Aqua awakens on the Destiny Islands, where she initially thinks that it has fallen to darkness once more. However, Riku tells her that she's back in the Realm of Light, and Sora, Donald, Goofy, Riku, Mickey, and Aqua share a long hug over freeing her...
