Completion bonuses
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.

Bonus features
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.

Also, 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.

Have a completed saved game from Xenosaga Freaks to unlock Hakase/Professor's special sub-event with the swimsuit.

Hangover Drink GS combination
The 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.