Reap The Rewards
On some parts of the adventure, failing a mission or retreating will force you to restart the mission but your experience points will carried over from your last attempt. Failing several times to accrue experience will help you in the long run.

Unlock Alternate Ending
In part 12 of the game, kill more enemies than the Mars Angels for one extra panel in the ending.

Weird Attack
In the mission where you rescue Robin and you get your Orbital Frame, go to the factory with Edge. Then put any LEV directly in front of where Ned will appear. When Mebius appears, she will be behind the LEV so she will not be next to Ned, but she will use Split Sword anyway, which would not normally happen. This can also happen in other instances if you have completed the game and know where to mess with the game.