Bonus features
Have a saved game from Xenosaga: Episode 1 to unlock new features when starting a new game.
Completion bonus
Successfully complete the game and create a cleared save game when prompted. Load the cleared saved data to begin the game at the Save Plate in the Elza. New dungeons and events will be unlocked.
Secret Dungeon #2 - Industrial Facility (Character)
Use the UMN again, and select the second option which is MOMO's Encephalon (Summer). Head to the right for the next area. Continue to the right to the next area. Now in this area, go right a bit, then NW for a little house. Destroy it and reveal yet another Forbidden Device. With the Sequencer C, dive into the Encephalon for the second secret dungeon. Defeat the boss in this area to activate an elevator that leads you to the end area of the secret dungeon. Within this area, you will need to activate G2 Campaign No.21 to do the puzzle here. Clear the puzzle and get the Mufufu Book along with Sequencer A.
Secret Dungeon #1 - Desert (E.S)
Load the clear data and talk with Hakase/Professor that's near. Now talk to Captain Mathews and select the second option to get back to Second Miltia to look for Kyouju(another word for professor in Japanese). While you are Second Miltia, go to the first sector of the street area. Now head up the stairs that's near the save and UMN plates. Take the room to the left. Enter the room and talk with Kyouju. You will get "Sequencer B" and now head to an UMN plate. Select the fifth option which is the Ormus Mobile Fortress. At the first intersection, head to the right then up to check out the Forbidden Device. Select the first option to dive into an Encephalon. You will be at the first secret dungeon where you use your E.S. Defeat the boss in this dungeon and get Sequencer C for the next dungeon.
Skill Points Bonus
If you load the Xenosaga Episode I or Xenosaga Episode I Reloaded clear data, not only will you get the swimsuit skills for Ziggy and KOS-MOS, your characters' starting Skill Points will also be based on your characters' levels when you beat the game of Xenosaga Episode I or Xenosaga Episode I Reloaded. The formular is character level * 30 + 600. Hence if your characters' levels are at Level 99 when you beat Episode I, they will have 99 * 30 + 600 = 3570 Skill Points to begin with. Xenosaga Freaks data will get you the swim suit for Hakase/Professor BTW.