Have a completed saved game file from Xenosaga Freaks to unlock Hakase/Professor's special sub-event with the swimsuit. Have a saved game file from Xenosaga: Episode 1 or Xenosaga 1: Reloaded to unlock KOS-MOS' and Ziggy's swimsuits when starting a new game. Additionally, your characters' starting Skill Points will also be based on your characters' levels when you completed Xenosaga: Episode 1 or Xenosaga 1: Reloaded. The formula is character level * 30 + 600. For example, if your characters were at level 99 when you completed Xenosaga: Episode 1, they will have 99 * 30 + 600 = 3570 Skill Points to begin with.
Successfully complete the game. At the end, you will be prompted to make a clear data file. Do so, and save over your existing or last one if desired. Load the clear data. You will end up at the Save Plate in the Elza with Hakase/Professor blocking the way. The following events and extra dungeons can only be unlocked by doing this. With this, your UMN will also have the map "Omega System". However, even this is like an epilogue because you can now trigger all these events and secret dungeons, you are still considered to be before the end of the game, before going to the Omega System.
Secret Dungeon #1 - Desert (E.S): Load the clear data and talk with Hakase/Professor that is near your starting point. Then, 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. Then, climb up the stairs that is near the save and UMN plates. Take the room to the left. Enter the room and talk with Kyouju. You will get "Sequencer B". Go to an UMN plate. Select the fifth option, which is the Ormus Mobile Fortress. At the first intersection, go 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.
Secret Dungeon #2 - Industrial Facility (Character): Use the UMN again and select the second option, which is MOMO's Encephalon (Summer). Go to the right for the next area. Continue to the right into the next area. In this area, go right a short distance, then northwest to rech a little house. Destroy it to 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 #3 - Sky Ruins (Character): Go to Kyouju's place in the first section of the street area on Second Miltia. Go downstairs and check the Forbidden Device here. Thanks to the Sequencer A, you can dive into the Sky Ruins which is the third secret dungeon. Defeat the bosses In this area to get to the item chest that contains Decoder 12. Use it to open a red door that is also in the Sky Ruins to get Sequencer D.
Secret e-mail address: After defeating Dark Erde Kaiser, go onboard the Elsa to its Robot Academy. Talk to Campari to get a real e-mail address to get some "clues." After getting these three "clues," go to the address given to input the three codes to unlock some Xenosaga: Episode 2 extras.
Vs Black Erde Kasier: Go to the first Secret Dungeon - Desert and go all the way back to the room with an item chest and a Forbidden Device. To the north of this room, you can get off your E.S. Continue along the path. With the Sequencer D, you can dive into another secret location, the Space Coliseum. In here, talk with Black Hakase/Professor to trigger an event, and eventually you will end up fighting Black Erde Kasier.
Extra Boss #2 (Baal Zebul): You may fight Baal Zebul in the Old Miltia (14 years ago) area. He is at the very end of the area, right after the second save point. His stats are as follows:
- HP: 99,999
- Exp: 99,999
- C Pts: 9,999
- S Pts: 9,999
- Break: BCBC/BBBB/CCCC (changes)
- Weakness: Ice, Pierce, Strike
- Exp: 99,999
Extra Boss (Mikumari): You may fight Mikumari in the Desert secret dungeon. In addition, you must have defeated Dark Erde Kaiser. Mikumari will appear where you fought Scarabeille. It is an E.S. battle because the Desert is an E.S. dungeon. When fighting Mikumari, it should be noted that when it is in "Pure" mode, if you cast "Down"-type ethers (Down Force, Down Ether, etc.) on it, it will heal you (either Heal All, Medica 2, or Refresh L). Its stats are as follows:
- HP: 96,000
- EXP: 68,000
- Weakness: Beam, Aura, Fire, Strike, Ether-based attacks
- EXP: 68,000
Extra boss (Phobos Rigas): Use the UMN to go to the restricted area on the Dammurung. Where KOS-MOS's ship used to be, there is a Gnosis, a Boss called Phobos Rigas. Its rare item is Auto Recover (E.S. accessory) and its normal item is EMAX300 (also E.S. accessory). With that EMAX300, you can put one on each E.S, allowing all three to use their special moves. Its stats are as follows:
- HP: 55,555
- Exp: 85,000
- S. Pts: 4,000
- C. Pts: 6,800
- Break: CBBC
- Exp: 85,000
Get more than one Awakening II: It is possible to steal Awakening II at the start of your battle against Orgulla, and once more each time she uses the "Manes Restraint Program" ability and changes back to her starting form (with the green sword).
Get more than one Awakening III: When you are fighting Magulis in Labyrithos, you can also steal from his "Shadow" every time he creates ones to get Awakening III and Skill Drug E. The Awakening III can be sold for 500000 to repay the debt (G2 campaign #32).
Get more than one Awakening IV: You can steal the Awakening IV from the Patriarch in Omega System and then fight him again with the clear save file to steal more.
The correct combination for the Hangover Drink GS campaign is: 3-2-2.
The correct combination of blocks to shoot in the puzzle at the end of the secret industrial factory level, is: blue, gray, yellow, orange, red.