A triumphant return from a monster-infested forest marks the completion of the 16-year-old hero's coming-of-age ceremony. However, the hero's joy is short-lived as a young village girl is found to be afflicted by a mysterious illness known as "crystal sickness." Determined to obtain the cure, the hero steps out of the secluded village for the first time, only to discover a world in which crystals are merely artifacts of the past and no longer exist....

A thousand years have passed since the events of the original Final Fantasy Crystal Chronicles. The destruction of Yuke Crystal during the Great War had at once brought the victorious Litlty Tribe prosperity, the defeated Yuke Tribe apparent annihilation, and the world a new age of science and reason....