Alright, so I finally visited the Wikipedia page for the game. Under plot:
"A thousand years have passed since the events of the original Final Fantasy Crystal Chronicles. The destruction of the Yuke Crystal during the Great War, with the Yukes suffering apparent annihilation, had at brought the victorious Lilties dominion over the world as they bring it into a new age of science and reason with the use of magic outlawed and rule over the Clavats and few Selkies who comply to the new order. In this new era exists a rare breed of powerful beings called "crystal bearers", whose seemingly magical abilities have led them to be feared and scorned by the public. The young mercenary 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 suddenly besieged by a 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..."
I still maintain the Lillties are going to be the real bad guys here, and the Yuke is really just a freedom fighter or something. I mean, the Lillties are conquering the world and oppressing people! All they need is to have a Fu Manchu and you've got textbook Bad Guys!
