Complete the game and create a cleared save game when prompted and new dungeons and events will become unlocked when you begin a new game. In the new game you will start at the Save Plate in the Elza and your UMN will now have the map of the Omega System. New features are also unlocked when you start a game with data from other Xenosaga games on your Memory Card.

The only correct combination for the Hangover Drink GS campaign is 3-2-2.

At the end of the secret Industry Factory level the correct combination of blocks to shoot in the puzzle is Blue, Gray, Yellow, Orange, Red.

Unlock Ziggy's Swimsuits:
Have a saved game from Xenosaga: Episode 1 or Xenosaga 1: Reloaded to unlock KOS-MOS' and Ziggy's swimsuits when starting a new game.

Unlock Hakase's Special Sub-Event:
Have a completed saved game from Xenosaga Freaks to unlock The Doctor's (Hakase) special sub-event.