Play as a Kronnhunter
Right when you start the game shoot nothing only the first 3 Staar Team members you see. The game will restart and you will now be playing as a Kronnhunter.
In level 2 shoot out all the upper windows of the far back wall in the Hanger and you'll get a secret room.
To get the best ending make sure you shoot off all the panels on the Mothership. To get the worst ending let the mothership escape without shooting off any of the panels.
There is a secret stage called the Chow Palace. First near the beginning of the game is a part where you ride through the complex in a jeep. After that you enter the office. Near the end of the Office where you go through the fire there is a part with paintings on the walls and two office doors. Shoot all the paintings and both office doors.
Secret Stage 2
On the last level where the aliens are throwing barrels at you destroy all the aliens the barrels and ammo boxes. In the large room with all of the trucks and helicopters in it shoot all the lights and you'll find a secret room called Headquarters. When riding the jeep shoot all of the yellow barrels. You should get a secret room called Eggcellent.