Shotgun
At the pause screen, press Triangle, Square, Triangle, Left, R1 to start with a shotgun.

Endings
For the best ending, shoot off all the panels on the Mothership. For the worst ending, let the Mothership escape without hitting any panels.

Rebel Kronn Hunter mode
Shoot the first three S.T.A.A.R. team members at the beginning of the game. If done correctly, you will enter Rebel Kronn Hunter mode.