Aqua’s story starts off like everyone else’s. She gives Ven and Terra a Wayfinder each the night before the big test. The next day, Aqua becomes a Keyblade Master while Terra doesn’t pass the test because he couldn’t control the darkness inside him. Eraqus then sends Aqua and Terra on a mission to deal with the Unversed and find Master Xehanort. Once Terra is gone, Master Eraqus asks Aqua to watch Terra closely and to bring him back as soon as it seems like he can’t handle the darkness. As Aqua and Master Eraqus walk outside, they see Ven leaving after Terra. Eraqus urges Aqua to bring Ven back as quickly as possible.
Aqua first visits the Castle of Dreams where she runs into Terra upon her arrival. Aqua warns Terra that Ven left after him. Terra then informs Aqua he learned that Master Xehanort is looking for pure hearts before leaving. Aqua walks in the ballroom right as Lady Tremaine and her daughters leave. She senses something very wrong coming from those ladies and decides to investigate. Arriving in front of Lady Tremaine’s house, Aqua senses darkness inside and wishes to fight it off, but she is stopped by the Fairy Godmother. The Fairy Godmother says it’s dangerous to fight darkness with light since they go hand in hand; you can’t have one without the other. The Fairy Godmother then tells Aqua that a friend of Cinderella is trying to keep her light from fainting, but he needs help so she shrinkes Aqua down and sends her in to help Jaq. Inside, Aqua helps Jaq get the key to Cinderella’s door and then, back in her normal height, she distracts the Grand Duke to give time to Cinderella to come down and try on the glass slipper.
Aqua then finds herself in the Dwarf Woodlands. She comes accross the seven dwarves’ home where they’re surrounding a casket with a girl inside. Aqua learns how Snow White was tricked into taking a bite of a poisonous apple and now lays dead inside the casket. Aqua tells the dwarves she’ll go to the castle to try and fix this. On the way, she meets a Prince that’s looking for Snow White and she tells him where he can find her. In the Queen’s chamber, Aqua doesn’t find the Queen but is instead absorbed by the mirror just like what happened to Terra. After fighting the mirror, Aqua returns to the dwarves’ home where she witnesses the Prince kissing Snow White and then Show White waking up.
In the Enchanted Dominion, Aqua arrives when Aurora’s heart is released. Aqua decides to investigate where the light came from and finds Ven arguing with Maleficent about how Terra couldn’t have been the one that stole Aurora’s heart. Aqua reassures Ven by telling him Terra would never do such a thing. She then asks him to return home with her, which he refuses and leaves. Maleficent then tells Aqua she could use her help to collect the pure hearts, but Aqua refuses and is sent in the dungeon. There, she meets Prince Philip and learns he got capture while trying to free Aurora from her deep slumber. Together, they make their way out of the castle and fight Maleficent in her dragon form before arriving at the castle where Prince Philip kisses Aurora and she wakes. Aqua then leaves the castles and sees Maleficent again. She tries to convince Maleficent that she will never be able to overcome a heart filled with light. Maleficent then tells Aqua she must not forget that as long as there is light there will be darkness.
In Radiant Garden, Aqua makes her way to the castle where she saves a little girl with the help of Mickey. They both agree there’s light in little Kairi and that they should protect her. mickey’s star shard then sends him off some play else. Aqua casts a spell on Kairi so that, if she’s ever in trouble, the light within her will bring her to someone else’s light that can protect her. Aqua then follows an Unversed and meets Ven and Terra that had been chasing their own Unversed. After defeating the Unversed, Terra finds out Aqua had been spying on him and leaves. Aqua then finds herself fighting the masked boy before Ven catches up to her. She tells him to go home but he still refuses and tells her she’s changed since becoming a Keyblade Master.
In Disney Town, Aqua is asked to play Fruitball to defeat the Unversed that have been ruining the game. Aqua then attends the Million Dreams Award ceremony, which actually goes to her, Ven and Terra. Pete is so mad that he finally gets on Minie’s nerves and she sends in him prison. There, Pete is delivered by Maleficent with the agreement that he’ll do what ever she says.
At the Olympus Coliseum, Aqua learns that Terra was there and had won the games. Phil convinces Aqua that Terra might come back to defend his title if she were to join the games. She decides to enter and fights her way through to finally fight against Zack in the semi-finals. After defeating Zack, Aqua thinks she’ll go up against Terra but she actually goes up against Hades and a giant ice monster.
In Deep Space, Aqua is brought in front of the Grand Councilwoman where she volunteers to take care of the Unversed infestation and to look for Experiment 626 and Dr.Jumba. Aqua stumbles upon 626 while he’s desperately searching for something while saying “Terra”. Aqua isn’t able to catch him long enough to ask him how he knows Terra so she continues her hunt outside. There, she finds a pretend Wayfinder she thinks might belong to 626. Aqua finds 626 and gives him back the Wayfinder before Captain Gantu arrives to neutralize 626. Aqua fights against Gantu and defeats him. Before he can do anything else, the Grand Councilwoman stops him. Aqua then convinces her that 626 might not be as dangerous as she thinks he is.
In Neverland, Aqua follows a treasure map with Peter Pan and the kids. They reach a very tall waterfall where the kids doubt they can fly all the way up. Peter Pan seems to force them up, but once they’re up there, Aqua sees that Peter was actually giving them courage. Aqua and cie then find themselves in front of Captain Hook claiming the treasure as his. When he opens the chest, he finds only what he says is junk. Peter gets mad and tells him it’s not junk, it’s their treasure. Before Hook can retaliate, he hears the crocodile and runs away. Aqua sees Ven’s wooden sword in the chest and Peter tells her he left it there and said he would visit them again someday. While Peter and the kids leave, Aqua senses a dark presence and goes her own way to investigate. She finds herself fighting Vanitas again after he destroys Ven’s wooden sword.
Aqua then follows a light in the Lanes Between and lands in Destiny Islands where she meets Riku and Sora. She wanted to bequeath the power to one of those boys, but before she could she sensed Terra had already bequeathed the power to Riku. Aqua thinks there should only be one in a friendship with the power to spare them from what was going on between her and Ven and Terra. So she doesn’t bequeath the power to Sora, but instead asks him to look after Riku and keep him safe.
Aqua then finds Micky in the Lanes Between and brings him back to Master Yen Sid where she learns that Master Eraqus had been struck down by Xehanort and Terra. She decides to meet Terra in the Keyblade Graveyard and face him.
There, she gets confirmation from Terra that Master Eraqus was struck down by him. He tells her he was protecting Ven and that he was tricked by Xehanort. Ven then arrives and tells them his story before asing them to put an end to him. Xehanort arrives with Vanitas before Aqua and Terra can do anything and the fight begins. After getting seperated, Aqua finds herself fighting against Braig. After defeating him, Braig says it didn’t matter because he was only buying time. Aqua runs back to a frozen Ven where she gets hit on the head by Vanitas. She wakes up in Mickey’s arms and sees Ven nearby holding the X-blade. When she tries to talk to him to make sure he’s okay, Vanitas’ voice comes out of Ven’s mouth and tells her he has the control now. Aqua tries to fight off Vanitas, but is unable to win against the X-blade. She clutches her Wayfinder while asking for strenght. Her keyblade starts glowing and she finds enough strenght to give a final blow to the X-blade, cracking it and making it go haywire. The X-blade releases a torrent of energy that swallows everything. All that Aqua can do before being swallowed is grab onto Ven’s hand. She wakes up in Yen Sid’s tower with an unconscious Ven by her side. She learns that Micky found them in the Lanes Between and brought them to safety. Yen Sid tells Aqua that Ven’s heart was sleeping and hanging the balance between light and dark, and he needed her to believe in him so that her light could guide him back towards the light. Mickey assures Aqua that his light would help guide Ven back as well. Aqua then tells him she’s sure Terra’s light would help too, even though he was still missing.