For the best ending, shoot off all the panels on the Mothership.
Shoot the first three humans you see without hitting anything else. When you hit the third human you will be taken into ''Kronn Hunter'' mode with messed up colors and a different ending sequence.
After riding through the air field and grabbing the ladder that's hanging from the helicopter, look closely for paintings hanging on the office walls. If you shoot all the paintings, and both office doors, a frightening, yet funny, room will be revealed.