With Ventus unconscious, Aqua carries his body outside the Mysterious Tower, but has no clue where to go. Summoning his Keyblade, Ven opens a door to the Land of Departure, where Aqua finally sees the ruins of her home for the first time, alongside Eraqus's fallen Keyblade, the Master's Defender. Carrying Ven's body to the throne room, Aqua remembers something Eraqus had told her:
With his words in mind, Aqua uses the Master's Defender to seal the Land of Departure, transforming the throne room into a white room with chains. She promises Ven that she will be back someday to wake him up after finding Terra, before leaving her home again. What was once an idyllic, stately land is now more ominous: the skies are darker, and the castle has taken on a more twisted form: a castle of oblivion. Just then, Terra's voice echoes, telling Aqua to put an end to him.
Aqua tracks Terra down to Radiant Garden, but what she finds is not Terra- it's Xehanort, having taken Terra's body for his own. She tries to jog Terra's memory, but Xehanort fully takes over, proclaiming that Terra's heart has been extinguished by his inner darkness. Summoning her Keyblade, Aqua prepares to fight Xehanort in one last clash, willing to return Terra to normal.
Eventually, after a lengthy duel, Aqua manages to prevail, thanks to Terra fighting against Xehanort's will. Xehanort is not having any more of Terra's resistance and brandishes his Keyblade to extract Terra from his body before sinking into darkness. Aqua, wanting to save what's left of Terra, jumps in after him and prepares to bring him out of the darkness. But there is no time left, so she sacrifices her Keyblade and armor to save him. As she falls, she laments not being able to save Terra.
Back in Radiant Garden, Ansem the Wise, Dilan, and Braig discover Xehanort, who can only recall his name. Satisfied, Braig decides to take Xehanort in, ordering Dilan to fetch Aqua's Keyblade and armor.
Within the Realm of Darkness, Aqua keeps walking onwards. Realizing how doomed she is, she decides to let the darkness swallow her, but is rescued by Terra and Ven's Keyblades. She begins to recall all the friends she made on her journey, and proclaims that there is a way to keep living.
At the Destiny Islands, as Sora and Riku prepare to head back home, Sora begins crying without knowing why. Riku explains that someone might be hurting outside, and has Sora call out to whoever is suffering. At the Dive to the Heart, Sora discovers Ven's damaged heart- it was Sora's newborn heart who had saved Ven when he nearly died, and since Ven has to sleep again, Sora offers to let Ven's heart sleep within his, giving Ven a second chance. Back in the waking world, Riku asks Sora if his idea worked, which Sora confirms.