What Could Have Been: The story was originally going to be very different for Xenosaga II and III before Executive Meddling caused the scenario writer Soraya Saga to be dismissed and the original script by Takahashi to be discarded. A portion of the old script was retained for the Pied Piper cellphone game. Among some of the things that were originally planned to happen for Episode II:
Citrine would reunite with her URTV siblings.
Shion's past history with Febronia.
Junior rapidly growing to an adult with both options available during battle.
The ghost of old Miltia.
The death of Sakura.
Brief reunion between the URTVS and grown-up Citrine.
Gaignun vs the Zohar emulators.
Junior and Albedo vs U-DO vs KOS-MOS 3rd armament.