A thousand years ve passed since the events of the original Final Fantasy Crystal Chronicles. The destruction of the Yuke Crystal during the Great War had at once brought the victorious Lilty Tribe prosperity, the defeated Yuke Tribe apparent annihilation, and the world a new age of science and reason. In this new era exists a rare breed of powerful beings called "crystal bearers," whose eemingly magical abilities have led them to be feared and scorned by the public. The young mercanary Layle is one such crystal bearer, who has been hired to escort the new passenger airship Alexis, the pinnacle of Lilty technology and a symbol of their current dominance. However, when the Alexis is suddently besieged by horde of monsters, Layle comes face to face with an adversary thought to have vanished from the pages of history, on a quest that may threaten the future of the world...
After the destruction of the Yuke Crystal, Lilty scientists studied the remaining shards to develop various technologies from the mystical power they possessed.
At the same time, people with superhuman, perhaps even magical powers began to appear sround the world. These being always had some part of their body that had turned to crystal, and were soon collectively referred to as "crystal bearers".
Was this an aberration brought on by the destruction of the Yuke Crystal? Or a side effect of manipulating a crystal's power? Or perhaps a curse left behind by the Yuke tribe?
Because there so few in number, the crystal bearerse never united as a single group, but there were individual crystal bearers that began abusing their powers, which in turn provoked an exaggerated response from some members of the lilty Tribe, who began hunting down bearers as criminals. Labeled as abominations and troublemakers, the crystal bearers were cast out of the "civilized" society.