Xenosaga Episode 2: Jenseits Von Gut und Bose Cheats

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.

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.

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.

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.