In a time, during the Age of Fairy Tales, the universe was one world divided into separate Unions in which Keyblade Wielders decide which one to go to. It is an age of peace and tranquility. However, this chapter comes to an end when its prophesied that an ill-fated Keyblade War will tear everyone apart and destroy everything. With the disappearance of the Masters of Masters and Luxu, the Union leaders began to tear each other's throats out. Rules are broken, fights and arguments become daily as the sun rising, and greed for the light only increases. Not only that but the suspicion of a traitor only deteriorates the fragile relationship of the Union leaders. And all Aina Mirai can do is sit and watch as the very future she foretold comes true before her very eyes.

There is only one thing standing between Sora's slumber and awakening; Roxas. Sakura leads him to his tragic end and is reunited with Sora as payment. However, this isn't a time to celebrate-Organization XIII is on the rise and they are getting closer and closer in achieving their goal of obtaining Kingdom Hearts for themselves, which Sora and Sakura must stop together. As the two head out on another journey while along the way, Sora looks for clues to the whereabouts of Riku and Kairi, which Sakura knows the answers to, but knows that she cannot tell as she made made promise to her dearly beloved not to until the time is right.

In a giant, lonely castle sits a bird, trapped inside her own cage. A white witch by the name of Naminè. As she sits, waiting for her saviors she is joined by another girl who both work under the mysterious Organization XIII. As the saviors make it to the top where Naminè sits, they are shocked to discover that she is joined by Sakura herself, in which both are used to achieve the Organization's goal. But, here's the thing; Sakura doesn't mind working for the forces of darkness.

On a remote island there lies four best friends longing for adventure outside their cramped lay island; Sora, Riku, Kairi, and Sakura. All get their wishes granted, but not in the way they imagined-Sora and Sakura are cast away into another world, Riku becomes puppet to the darkness and Kairi goes missing. Sora and Sakura go out on a journey together, equipped with a Keyblade for themselves and with the help of the magician Donald and Captain Goofy to find their missing friends where Sakura discovers her true identity of who she actually is.