This level is a quick break from the story and an excuse to have some fun just running around blowing sh*t up. It's one of the few extermination missions in M2. Some have guessed that this level was stolen from the defunct Marathon 20/10 Secnario Pack, since it shares several characteristics with several levels from the previous game.
When you beam in, there is an assimilated civilian in the northeast position. Head east to get into the "home base" room, which has every utility a Marine could ever need: Terminal, health, oxygen, pattern buffer. The terminal gives some more information about the Assimilated Civilians. "Watch for friendly fire"... Should have said that to the Bobs :P
When killing large groups of sims, be careful because their physics have been changed somewhat since Marathon 1. In M1, when they detonate their damage is inflicted on the very first frame of animation, at the exact moment of their death. This is calculated in the same frame that they died, so killing a group of sims results in them all going off at once. However, in Marathon 2, the explosion was moved to the second frame of animation, when they begin to burst. One side effect of this is that M1 sims explode at the exact spot they were killed every time, but if an M2 sim is killed with significant force it will be hurled through the air, land somewhere else, and then explode. So, when killing groups, be prepared to dodge dangerous corpses hurled in your direction by their exploding comrades.
What is the meaning of the mysterious underground room full of assimilated civilians and monsters? I believe it was meant to be a makeshift prison, into which all captive Pfhor and discovered Sims were herded when the Bobs took over this facility. The Sims would have to be captured through trickery rather than combat; since they are capable of living among humans they must be able to suppress detonation when required and the humans could capture them without letting them know that their secret's out, much like the sting operations real-life police often use to serve warrants (for example, Homer's "boat lottery" on a certain Simpsons episode). The two brown (security) Bobs outside the room on a ledge would have been serving as guards, they have a clear field of fire across the only way in or out of the room. (I'm ignoring the fact that the monsters teleport in; this may have been a mistake or a deliberate inconsistency meant to make the room more exciting.)
Near the end, in the room where the Shotgun is found, there are two switches hidden in the walls of the hallway. One of these drops a crushing platform on the monsters, one crushes the Bobs. Hit them both :P If you're playing co-op, this room actually has three shotguns, and there's an M-75 with ammo in the south dark room earlier in the level.
The exit terminal reveals more information about the mysterious AI, which is now named Thoth.
