- "The three of us will always be one."
Aqua is one of the main protagonists of Kingdom Hearts Birth by Sleep. From the view of the story, it is revealed she is one of the Keyblade Wielders before Sora. Like Terra and Ventus, it is her dream to become a Keyblade Master, a dream she is the only of the three to accomplish.
The only connection between her and Kairi is that Aqua met Kairi in Radiant Garden in Kingdom Hearts Birth by Sleep and put a protective spell on her necklace, which later brought Kairi to Destiny Islands. Kairi, by accidentally touching Aqua's Keyblade during this time, also inherited the Keyblade from Aqua.
Aqua, alongside Terra, is one of Eraqus's pupils. Like Terra, Aqua also had a dream of becoming a Keyblade master.
One day, a suspicious man named Master Xehanort arrived and gave Eraqus a new apprentice to work with named Ventus. Terra calls out to Aqua, telling her that a new apprentice had just arrived. While chatting with Ven, Aqua and Terra asked Ven about why he wanted to train to become a Keyblade master, but this question, as well as a few other questions troubled Ven, so much that he couldn't take the pressure. He fainted and shocked Aqua and Terra.
Eraqus tells Aqua and Terra that the reason Ven fainted was because he had amnesia. Aqua decided to look after Ven, in case he woke up. Many days passed, but despite Ven being unable to awaken, Aqua would not abandon him. One day, Aqua saw Ven open his eyes and regain consciousness, he was finally awake.
Since that day, she and Ven became close friends and rivals. Days have gone by, and she, Terra, and Ven became close like siblings, sparring with each other, sharing dreams and secrets, Aqua wanted to keep their bond strong, so one night, she surprised Terra and Ven with Good Luck Charms, made by her to commemorate their long lasting friendship.
The next day, she takes the Master Qualification Exam along with Terra, and becomes a Keyblade Master, although Terra fails it due to his heart having darkness within it. After Terra and Ventus left, Aqua was the last apprentice to be sent by Master Eraqus to bring Ventus back to the Land of Departure. But before she left, Eraqus wanted to ask Aqua to keep an eye on Terra, to make sure he is alright, and stays safe from the darkness in his heart. If Terra's heart would become to close to the darkness, Eraqus needed Aqua to bring Terra back immediately.
Aqua, Ven, and Terra come across many Disney characters along the way and fight of hordes of Unversed. Aqua later ends up at Radiant Garden with Mickey Mouse and meets the Princess of Heart, Kairi, who touched Aqua's Keyblade in fright, unintentionally performing a Keyblade Inheritance Ceremony. They protect her from a group of Unversed and in return Kairi gives Aqua flowers, which becomes the Keyblade, Destiny's Embrace. She also places a protective charm on Kairi to help her in the future. Aqua believes that their meeting may not have been a coincidence.
At one point Aqua and Terra come to Destiny Islands and meet two young boys by the name of Sora and Riku. Aqua sees the strong bond between the two friends and advises Sora to help Riku if he ever falls into darkness. Aqua later encounters an unconscious Mickey drifting in space and takes him to the Mysterious Tower, where she hears of Eraqus's death from Yen Sid and heads to the Keyblade Graveyard to meet up with Terra and Ven. They are confronted by Master Xehanort and his apprentice, Vanitas and a great battle takes place. After fighting Braig and then Ventus under Vanitas's influence, Aqua loses consciousness and she ends up at Yen Sid's Tower with Ventus, who has lost his heart. She takes Ven back to the Land of Departure and places his unconscious body in a throne. She takes Eraqus's Keyblade and transforms the world into Castle Oblivion to keep Ventus safe. She then tracks down a possessed Terra in Radiant Garden.
Failing to bring Terra back to his senses, Aqua fights and defeats Xehanort, who would have fallen into darkness if Aqua hadn't saved him by sending her armor and Keyblade with him out of the darkness. Now stuck in the Realm of Darkness, Aqua is attacked by several giant Heartless, but is saved by Terra and Ventus's Keyblades. She is then reminded of the people she's connected to. With renewed trust in her friends, Aqua continues on.
Aqua's armor and Keyblade were briefly seen in Kingdom Hearts II Final Mix. They reside in the Chamber of Repose, a room constructed by the Apprentices under Radiant Garden for an as of yet unknown purpose. Xemnas visits the armor often, calling it "friend" and talking to it for long periods of time. This has piqued the curiosity and suspicion of Xigbar who often eavesdrops on his conversations, and once shared this story with Zexion, stating that one time he heard "another voice" respond to Xemnas. In The World That Never Was, Sora encounters Xigbar, who mentions "other Keyblade bearers", referring to Terra, Aqua, and Ventus.
Aqua ends up at the Dark Meridian, where she meets Ansem the Wise, who was cast into the Realm when his [[Kingdom Hearts Encoder|machine] exploded. He reveals that in the Realm of Light, it has been almost eleven years, and he explains the events that have occurred in Aqua's absence, including the actions of Sora. Knowing that Sora will rescue her and her friends, she sheds a single tear, while uttering Sora's name with renewed hope.
Aqua is alluded to by Data-Naminé as one of those connected to Sora's heart and need his help, appearing as one of Data-Naminé's mental images. Later on, after Mickey informs Yen Sid that they have located Ventus's heart, Yen Sid concludes that Terra is the only one left to find, implying that they have already located Aqua.
Mickey mentions Aqua when he suggests that he help Sora and Riku inside the Dreaming Realm by following his heart's path, as Aqua told him long ago.
When Sora arrives at The World That Never Was, he is caught by the Organization and placed within a nightmare in which he chases after memories of Riku and Kairi. When he catches up to them at the Contorted City, the phantoms suddenly take the form of Terra and Aqua, while Sora himself takes on Ventus's appearance. Sora is confused, but the phantoms grasp his hand before turning back into Riku and Kairi and walking off again. As Riku attempts to wake Sora on his own side of the dream, Sora recalls when Aqua came to Destiny Islands, and nearly wakes up.
However, Ansem appears within Sora's dream at the last second and thrusts him back into the nightmare. Xigbar and Xemnas reappear within the nightmare to taunt him and lead him into despair by explaining the inevitability of their plan and playing on his insecurities, but a defiant Sora proclaims that while he may not have been chosen by the Keyblade, he will always be proud to be there for his friends, including Terra and all the others.