The friendly Gencorp troopers nearby should help to take out the aliens in your area. When they are done, collect the ammo and go outside. Kill the aliens in the pit; be careful though as it's easy to take a lot of damage here. Afterwards, use the comm terminal in the corridor and then ride the elevator to the top level. You'll be greeted by a number of monsters around the corner, and even more will join in from the small octagonal room. Now follow the corridor until you come to a large dark chamber. (Look out for lots of exploding boomers around here; although you don't have to exterminate them, they can be quite a pest.) Use the 1x recharger at the other end of the room first, if needed, before heading to the first available corridor to your right. In the wall behind door A there is a small door, and behind there's a small elevator leading to a higher corridor. When you reach the end of this corridor, jump towards the lava stream. Run upstream to a small niche on your left where a 2x recharger and a pattern buffer is located. When you're done there, continue on up the lava stream. At the end you will reach a large room with stairs around the walls. Go all the way up until you reach a room with a teleporter. Kill any aliens (the teleporter is optional should you feel the need to explore further), then head back down the lava stream.
Back in the large dark chamber again, the door to your left will have opened by now. Head on through the long corridor, cross the narrow path across the lava pool, jump across the lava river in the next area, and finally head up the circular stairway. Continue straight ahead until you reach switch 1. Flip it to open door A, then retrace your steps a little until you reach the lava pool. A platform will have dropped here, making the way back to the large dark chamber much easier. Recharge if necessary, then find door A. Behind it is a very large lava pool, with a ledge running around the walls. Follow this ledge to reach the corridor in the southern wall. The small stairway around the corner leads to a room with a pattern buffer and a 3x recharger.
Now take platform C to reach a small room containing some
ammo. Note that platform C stops as soon as you enter this
room; you won't be able to return to the area you've come from until
you've been to the end of the level, so take care from here onwards.
Head on to the diamond shaped room with a switch (switch 2) in
the central pillar. Flipping this switch will activate platform
B, which leads to the really huge final room. Take care of all
the monsters here, and check the comm terminal at the far end. If it
reports that there are still aliens active in the level, flip
switch 3 next to it to lower platform C; you can now
return to the main part of the complex and search out the surviving
aliens. When all the aliens are dead, the comm terminal will take you
to the next level, Damage Is Our Middle Name...