You've cleared out the large square hallway, including the aliens on that ledge, but now you don't see anywhere to go? Find the elevator that will take you up a level (activated by the switch near the light switch on one side of the level). Then, while running, jump across to the ledge, and head to the left. If done correctly, a door should have opened leading you into the next part of the level, with a supply of ammo just inside to the left.
Now you've cleared out the other square area, and are stuck down in a pit? Then go to the center of the west wall and look for a door. This will reveal a long corridor that will take you back to the first part of the level, and the door to the final room will be open.
As an added bonus, you can get to read the lyrics to the Durandel song! After you return to the first part of the level, redo the level (no monsters this time, of course), and when you get to the room with all the elevating platforms, go to the computer terminal and read what Durandel has to say. Note: make sure your shields are charged before reading, because Durandel will jump you from here to the next level.
Also within the elevator room is an ammo cache. The door is located just left and behind you from where you teleport in, but it will only open once you touch the left-hand wall near the teleport out of the level, so there is a lot of elevator timing and luck involved.
There is a second ammo cache, as well as another terminal, in the room with the slowly retracting door. The cache is located in the corner where you teleport into this room, but to activate, you need to grenade jump onto the lower right-most portion of the sniping ledge on the other side of the room.