Have a saved game from Xenosaga: Episode 1 to unlock new features when starting a new game.
Clear Data Ex Game
Beat the game first, and at the end, the game will ask you to make a clear data. Do so, and save over your existing/last one if you wish. Now load the clear data, and you will end up at the Save Plate in the Elza with Hakase/Professor blocking the way. There are events and extra dungeons can ONLY be unlocked by 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.
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.
Get all the hyper fertilizer you need
For GS campaign 10, you must find 5 hyper fertilizers along with the flower seeds. Instead of getting one hyper fertilizer from each of the npc's that carries it, you can get all 5 hyper fertilizers from one person. Go to the space port on second miltia, and talk to Rosa (the old lady by the save point). Talk to her over and over, and she will keep on giving you hyper fertilizer until you have enough.
Get Bathing Suits
Load a save file that's been beaten from the first Xenosaga game or Xenosaga Reloaded to unlock bathing suits for Kos-Mos and Ziggy.
Hangover Drink GS Combination
The only correct combination for the Hangover Drink GS campaign is: 3-2-2.
Industrial Factory Puzzle
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.
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.
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 #3 - Sky Ruins (Character)
Go to Kyouju's place in the first section of the street area on Second Miltia. Go down stairs 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's also in the Sky Ruins to get Sequencer D.
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.
Swim Suit Skills and Erde Kaiser Moves
Press Triangle to get into the menu, select 'Skills' then select anyone. Then Select Skill. Go down to 'Level 4', press 'Right'. You will see Class A to D. Press 'X' ONCE and press right to the Tutorial. Go through the whole tutorial. Once you are done, you initiated the bug/glitch. You should now see Class E to H for Class 4. Don't get out of the menu, it would disappear and go back to normal. If you learn any of these skills, you will get to keep them. From Class E to H, you will need 450 Class Points. But within each, you need zero Skill Points to learn all. Class G and H got nothing but you can still pretend to learn 'nothing'. Class F has 3 Erde Kasier Retsu/Extreme moves, one deals with slash damage to all, another one deals pierce damage to all and the last one deals thunder damage to all. All need 50 EP. For Class E, you have swimsuit skills and 3 more Erder Kasier moves, Erde Storm, Erde Beam and Erde Quake. For those without the Episode I clear data, this is helpful for you to get Ziggy and KOS-MOS' swim suit skills since they aren't found in the game of Xenosaga Episode II. And do remember these are Class Level 4 skills, you need to pass to Class Level 4 first.
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.
