Once upon a time the world was full of light, peaceful and beautiful. However - as it's human nature - people started to fight over it. Jealousy, anger and fear started to cover their hearts and eventually the world succumbed to darkness.
But there were still little bits of light left; inside the hearts of the world's children and together they defeated the darkness and recreated the world. However the world was still fractured into many, kept in a precious balance between light and dark. Those were the Keyblade Wars.
Now the Keyblade Masters are almost the only ones with knowledge of the pathways between the worlds and safeguard them and the balance of light and darkness to keep the world order.
At presumably young age Aqua becomes apprentice to Master Eraqus, living with him and her fellow apprentice Terra on the small world named 'Land of Departure', training to become a Keyblade Master. One day - about four years before the main story - another Keyblade Master, Master Xehanort, appears together with a young boy without memories and requests Eraqus to train him.
The boy, Ventus (nicknamed 'Ven'), became the third apprentice in the Land of Departure and started to learn alongside the other two. Though originally quiet and sad, over the time Ven turned into a cheerful teenager, who loves being together with others and is very attached to Terra in particular, while both Terra and Aqua have become very protective of him.
Time passes and eventually Terra and Aqua are ready to take the Master Exam. Just the night before the exam Aqua gives self-made, star shaped good-luck charms ("Wayfinder") to the other two, claiming that they would intervene their destiny forever.
On the next day, Terra and Aqua take the exam, under the watchful eyes of Master Eraqus and Xehanort. Later manipulates the first trial of the exam, in order to be able to examine the skills of all three apprentice. In the last trial, Terra and Aqua are pitched against each other in combat. In the middle of the fight for just a second Terra falls back on the 'darkness in his heart', which is the reason why Eraqus decides to allow Aqua to pass the exam, but to fail Terra and deny him the title of Master. Disappointed Terra leaves, ignoring Aqua's and Ven's attempts to cheer him up.
Just as Master Eraqus finishes instructing her in her new duties as Keyblade Master, the bells within the castle start to ring, signaling Yen Sid's attempt to contact Master Eraqus. Just as he leaves to talk to the former Keyblade Master, Terra returns, wondering about what is going on.
Eraqus reveals that Master Yen Sid had just warned him of a threat to the 'Princesses of Light', creatures that feed on negative feelings called the Unversed. Since he had not been able to contact Xehanort, Eraqus orders the two older apprentices to destroy the Unversed and to reestablish contact to Xehanort. He also tells Terra that this could be his chance to be found worthy of becoming Master after all.
Terra leaves and just as Aqua is about to follow, Eraqus calls her back, requesting her to keep an eye on Terra and bring him back to the Land of Departure should he find himself overwhelmed by the Darkness. Just as Aqua is about to leave towards the worlds herself, she sees can only watch as Ven decides to follow Terra out into the worlds and is ordered by Eraqus to bring him back as Ven is not allowed to leave the Land of Departure.
Aqua reassures him that she will make sure to return him and leaves for the worlds as well. She quickly locates Terra in the first world she visits, the Castle of Dreams. They trade information on Xehanort and Ven and Aqua is relieved when she realizes that he seems to have rediscovered faith into himself and his dreams. She assists Cinderella's mouse friend Jaq to release her from her room and helps her when she is assaulted by the Cursed Coach.
She continues to travel the worlds, eventually ending in the Enchanted Dominion, just in time to interrupt Maleficent as she ties to relay Ven's worry and doubt of Terra. She encourages Ven to believe into their friend and tries to persuade him to return to the Land of Departure. Ven refuses, taking off to once again search for Terra, and before Aqua can go after him, Maleficent sends her to the prison of her castle.
In prison she meets Prince Phillip, whom she assists in escaping the castle and breaking the curse on the Kingdom by helping him defeat Maleficent in her dragon form. However the evil fairy succeeded partly at least, as Aqua starts to doubt Terra's actions.
As she once again continues her travels, Aqua spots Terra in the Lanes Between and follows him to Radiant Garden. While searching the world for him, Aqua arrives just in time to see a young girl be attacked by the Unversed. Uncertain how to fight them while protecting the girl, Aqua is almost hit herself, if not for the sudden arrival of King Mickey. After bringing the girl to safety, Aqua and Mickey join forces to defeat the Unversed.
After a short introduction, Mickey's starshard activates, sending him away and leaving Aqua and the girl behind. The girl, whom Aqua senses a great light in, introduces herself as Kairi and gives Aqua flowers as a thanks. Before Aqua can talk with her about her light, her grandmother calls for her. Just before she leaves Aqua places a protection spell on her, so that she would be lead towards someone who would be able to protect her, if she ever were to find herself in trouble.
Just as she watches Kairi and her grandmother leave, Aqua notices a large Unversed. As she follows it, she is reunited with Ven and Terra and together, they defeat it easily. After getting passes for Disney Town from Ven, Aqua once again tries to convince him to return home. In the following discussion her doubts of Terra and Master Eraqus' requests to her to watch over Terra and bring Ven back are revealed. Terra leaves, declaring that he will walk his own path now and Ven follows him.
On the main plaza, Aqua then encounters the boy with the mask, Vanitas, whom Ven had mentioned and fights him. She just so manages to defeat him, but before she can take of his mask, Vanitas laughs and jumps up again, retreating into the dark, saying that Aqua is worth to be kept around as "back up". Ven reappears not too long after that, just as Aqua realizes how much danger Vanitas towards both her friends is. Since Terra has already taken off, she once again asks Ven to return to the Land of Departure and then takes off towards the worlds again.
As she travels, Aqua starts to realize that perhaps she needs to let Terra and Ven go their own way for now, though she continues to worry for them. Eventually she once again fights Vanitas in Neverland, just barely defeating him before losing consciousness herself, relieved that he would not be able to harm her friends again.
When Aqua continues to travel, the light guides her to Destiny Islands, where she meets two children - Sora and Riku. Sensing the light in both of them, she notes the similarities between them and respectively Ventus and Terra. Originally she intends to make Sora her successor, but ultimately decides against it when she feels that Terra had already passed on the Keyblade to Riku as she feels that one Keyblade is enough burden for any friendship. Instead she asks Sora to watch out for Riku and stick to him, especially should he end up stumbling into a dark path.
As she leaves Destiny Islands, she finds Mickey floating in the lanes between and brings him back to the Mysterious Tower. There Yen Sid tells her of Master Eraqus' death and that Xehanort and Terra were both involved. Denying Terra's involvement, Aqua asks for his whereabouts, learning that he is on the way to the Keyblade Graveyard.
In the plains of the Graveyard, she encounters Terra, who confirms Yen Sid's news and his involvement, saying that he was tricked into fighting their master by Xehanort. Even though he swears that he won't be fooled or used again, Aqua warns him to be wary of his anger and hate of Xehanort as it will only lead him astray again. Before Terra can answer, Ventus arrives, telling them of Xehanort's plan to make him and Vanitas fight in order to create the x-blade. In order to keep that from happening Ven asks the both of them to put an end in him.
Before they can answer, Xehanort and Vanitas arrive, provoking all three of them into battle. Terra takes off in order to take on the old Master and Ven follows him, hoping to help, but is frozen into an ice stature by Xehanort. Aqua just so manages to catch him as his frozen form falls down the cliff, starring up terrified as she sees Kingdom Hearts rise.
Just as she is about to take care of Ven, Braig arrives, provoking her into a fight by suggesting that she will soon have to fight Terra as he will succumb to the Darkness. After being defeated, Braig takes off, revealing that he was meant to act as distraction. Just as Aqua is about to return to Ven, Vanitas arrives and knocks her out from above.
Unconscious, Aqua remembers Ven's word, asking her to put an end in him. When she awakens, she learns that Mickey has come to the Keyblade Graveyard as well and together they start looking for Ven.
Ven is quickly found, but as it turns out he had fought and was possessed by Vanitas in the meantime, creating the x-blade. Together with Mickey she manages to weaken him, but when everything seems hopeless, Aqua calls for Terra and Ven's strength, causing her Keyblade to glow. With one final strike, she defeats Vanitas and destroys the x-blade.
As the x-blade falls apart, Aqua just manages to reach Ven's unconscious body and both of them are blown into the Lanes Between. Found by Mickey and transported by his starshard, Aqua reawakens in the Mysterious Tower. Yen Sid tells her that Terra had disappeared without trace, that Ven's heart had gone to sleep and left his body and that it only return if Aqua believes in him.
Follow Yen Sids advice, Aqua takes off with Ventus, following the light of his Keyblade. Guided to the Land of Departure, she finds their home torn apart by the darkness and their Master's Keyblade Master Keeper abandoned on the ground. Using Master Keeper, she transforms the Land of Departure into a safe haven for Ven, where he can stay until she finds Terra.
As she leaves the newly formed Castle Oblivion, she hears Terra's voice calling faintly, asking her to put an end to him. She follows it to Radiant Garden, where she encounters a changed Terra. Realizing that he isn't Terra at all but Xehanort, Aqua demands him to release Terra. Battling him and his Guardian, Aqua eventually manages to touch and awaken Terra's heart long enough for him to use Xehanort's Keyblade on his body, hoping to cast out his heart. Instead however both their memory is locked away and Terra's body is drawn into the Realm of Darkness.
Aqua follows and catches him, but realizes that only one of them will be able to return to the Realm of Light. Giving up her armor and her Keyblade Stormfall, she sends Terra's body back and lets herself fall down into the Realm of Darkness.
Wandering the dark parths for an unknown time, she eventually encounters a group of Darkside appear and just as Aqua is about to give up, wondering if she shouldn't just fade into the darkness, the Keyblades of Terra and Ven appear, defeating the Heartless. Encouraged to keep going, Aqua swears to return home one day.
As she wanders the Realm of Darkness, guided by the light of her Wayfinder, Aqua witnesses a door to the Realm of Light open and the Darkness escaping through it. Trying to investigate the event, Aqua is attacked by a strong, red eyed monster, which she barely manages to defeat. As the dust from the fight settles, she suddenly sees the remains of the Cinderella's world, Castle of Dreams, standing in the Realm of Darkness.