What the hell happened?

Xenosaga Episode II: Jenseits von Gut und Bose
PS2 / Namco
February 2005

The second game opens with a flashback to the Miltia Conflict. Chaos and a Realian named Canaan are sent by the Federation in a new mech, the ES Asher, to find and recover the URTVs amid the warfare. Along the way they run into a Federation soldier named Jin Uzuki... who happens to be Shion's older brother. Unfortunately, as they arrive at the facility, the only survivors are Jr. and Gaignun. The flashback ends with a furious swordfight, when Jin is confronted by Margulis, his old superior and one of the most frustrating villains of the original game.

A new faction in the story reveals itself - the Immigration Fleet Ormus, the religious faction that supports U-TIC. Heading the church is the Patriarch, who commands the U-TIC army as well. It seems the Immigration Fleet and the Federation are at an uneasy truce - both are eager to get their hands on the data within M.O.M.O. to reopen the pathway to Old Miltia.