Keyblade wielder Aqua is no stranger to tragedy. A long time ago, when she was 17 years old, her master and teacher was slain in cold blood, her home was destroyed, and she lost her two best friends and fellow Keyblade wielders Terra and Ventus following a great battle, while she was left trapped in the Realm of Darkness with no escape.

10 years later, the villainous Keyblade master, Xehanort, and his other versions and incarnations of himself are stirring up trouble, including Xemnas, the leader and Lord of the Nobodies, The World That Never Was, and the Organization. After a humiliating defeat in a duel against the young Keyblade Hero, Sora, Xemnas (and fellow Organization member Xigbar) falls out of favor with Master Xehanort and is cast out of his secret Organization. Hoping to regain Xehanort's favor and be reinstalled as one of his secret Organization members, Xemnas accepts a deal with Xehanort: If he can find Aqua, plunge her heart into darkness, and bring her to Xehanort's side, he will reinstall Xemnas and Xigbar as members of his Organization. However, knowing of Xemnas' rebellious and ambitious side, Xehanort adds another requirement to his deal: Xemnas also has to marry Aqua.

Now forced into a cold and heartless marriage with Xemnas and made to endure a lifetime of living amongst Xemnas' fellow Organization members and subordinates, Aqua thinks she will never know happiness again. However, things begin to change when she learns of the Organization's plight in the Realm of Light as shunned members of society, and that all the Organization members seem to want is to regain their hearts and become whole again. Feeling pity and compassion for the Nobodies and perceiving their ultimate goal as benign, Aqua offers to use her ability to wield the Keyblade to capture hearts for the Organization. In doing so, she earns their trust, favor, approval, and respect.

But there's something else that also begins to change: Aqua's relationship with her new husband, Xemnas. Initially cold, distant, and unkind towards Aqua, Xemnas' uncaring and cold personality begins to thaw when Aqua's actions and kindness catch his eye and intrigue him. In time, a special bond and connection begins to form between Xemnas and Aqua – and it changes their lives and views of one another forever.