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.

Bad parents
Back in the present on Second Miltia, Shion and chaos reunite with Jin, who has been living on the planet, while M.O.M.O. and Ziggy meet up with Juli Mizrahi, Joachim's wife and head of the division which ordered M.O.M.O.'s rescue. As M.O.M.O. is modeled after the Mizrahi's late daughter Sakura, both physically and mentally, M.O.M.O. herself feels that Juli is her mother. Juli appears to find M.O.M.O. completely repellant, on the other hand.

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.