Before her introduction in Kingdom Hearts: Birth by Sleep, Aqua made small appearances in the secret endings from Kingdom Hearts II and its re-release, Kingdom Hearts II Final Mix. Both events depicted Terra, Ventus and her fighting Xehanort and his apprentice Vanitas. Moreover, her Keyblade and armor appear in a room from Radiant Garden in Kingdom Hearts II Final Mix, which Xemnas, the "Nobody" of Xehanort, often visits calling the armor "friend".
In Birth by Sleep, Aqua appears as a Keyblade apprentice in Land of Departure training alongside Terra and Ventus to gain the title of Keyblade Master. Aqua takes the Mark of Mastery exam along with Terra and becomes a Keyblade Master. When Xehanort goes missing, Eraqus instructs Terra and her to find him while also protecting the worlds they visit from creatures known as the Unversed. Following Terra's departure, Eraqus asks Aqua to watch over Terra to see if he succumbs to his inner darkness and also bring back Ventus who suddenly left the world. As she travels across the worlds, Aqua starts doubting about Terra's actions in the worlds, while Ventus decides not to return home until Terra is safe. When she meets Yen Sid, an acquaintance of Eraqus, Aqua is told that the latter was killed by Xehanort with Terra's assistance and goes to the Keyblade Graveyard to face him. Later, Terra explains to her how Xehanort tricked him into fighting Eraqus, while Ventus reveals that Xehanort plans to use him and his apprentice Vanitas to create a Keyblade known as the χ-blade. The three are then confronted by Xehanort and Vanitas, and proceed to battle. When Terra goes to battle Xehanort, Vanitas takes possession of Ventus' body to create the χ-blade. With help from King Mickey, Yen Sid's student, Aqua fights the possessed Ventus until the χ-blade explodes. After learning that Ventus has lost his heart while facing Vanitas, Aqua locks his catatonic body in Castle Oblivion created from the ruins of the Land of the Departure with Eraqus' Keyblade. Aqua then tracks down Terra to Radiant Garden, only to find that he was possessed by Xehanort. In the ensuing battle, Terra's presence manifests, causing Xehanort to stab himself in the internal struggle and fall into the Realm of Darkness. However, to save Terra's body, Aqua saves him by sending her armor and Keyblade with him back to Radiant Garden. As a result, Aqua ends up trapped in the Realm of Darkness. Sometime after the events of Kingdom Hearts II, she meets Ansem the Wise, the former ruler of Radiant Garden, and learns about the events that occurred in her absence regarding Sora, the new Keyblade bearer. Knowing that Sora will rescue her friends, Ansem, and herself, Aqua sheds a tear and utters Sora's name with renewed hope.