Despite life on Destiny Islands being one of comfort and ease, three friends, Sora, Riku and Kairi, long to explore the many worlds beyond it. One fateful night, their wish is granted sooner than they anticipated when dark forces called "Heartless" invade their island. Overrun by these creatures, the islands are swallowed by darkness, taking Riku and Kairi with it. However, before Sora succumbs to the darkness, a blade of light manifests in his hands: the "Keyblade," granting him the power to vanquish the Heartless.

Meanwhile in the world of Disney, the residents are in a flurry over the disappearance of their king Mickey Mouse. Leaving only a note behind, Mickey explains that he has gone to investigate an imminent danger threatening all known worlds. Furthermore, he instructs his aides, Donald Duck and Goofy, to seek out the one carrying a "key"; the one who can save them from their crisis. Thus the pair set off on their search, the first stop—Traverse Town.

Sora awakens in the very same town, only to find it plagued by the Heartless. Although finding his friends is his main concern, as the wielder of the Keyblade he must accept the grand fate thrust upon him; many more worlds have come under attack, and he and the Keyblade are the only hope of liberating them.