What's this game called?

It's an old PC game that must've come out around the late 90's / early 2000's, you play as a spaceship with a skull on the front. The only thing I remember about it was you fly around inside this... building of some kind. And there were little red "beacons" that you can find or collect or something. I think the game was mainly about shooting stuff though. Any help would be reeeeeaaaaally appreciated!!!