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.