Unlock Shotgun:
Pause the game, then press Triangle, Square, Triangle, Left, R1.

Invincibility:
Pause the game, then press X, Circle, Circle, Triangle, Circle, X.

Best and Worst 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.

Secret Rooms
It seems only proper that a secret base contains secret rooms. Here's how to find them:

Level 1: Shoot both blue lights.
Level 2: Shoot out all of the upper windows of the far back wall in the Hangar.
Another can be found by shooting all the yellow barrels when you are the forklift.
Level 4: Shoot every yellow box while you're riding on the STAAR jeep
Level 5: Shoot the doorplate of the second door marked General Weatherby as the door is opening.
Level 7: Shoot all the yellow barrels at the first area where the four purple zombies are throwing barrels on the hill.

Kronn Hunter Mode
At the beginning of the game, ONLY shoot the first three STAAR team members you see. If you did this right you'll enter Kronn Hunter mode. In this mode, you are a mercenary from the Kronn hierarchy sent to sterilize Area 51 of the Kronn rebels. You will notice that the grenades, bullets, shotgun shells, and machine gun bullets have all taken on a Kronn form. You will also gain 20,000 extra points whenever your score is tallied, and you can shoot STAAR team members with impunity.

Baby Aliens
When you enter the building from the helicopter, shoot the exit sign when you see a purple alien and then shoot the first three lights. This gives you the opportunity to shoot baby aliens before they form.

Secret Level Skip
When you go to the main menu. Click on arcade then a screen with 2 boxes will come up that says shoot to select: beginning or warp ahead. click on the black area around the box were it is blank. It will then bring you to an area that is far into the game.