Objective: Extermination
You arrive in one of Troy Colony's main administrative facilities...
After using the comm terminal, leave the room and turn right. You are now outside the Command Complex. Flip switch 1 located in the high-placed room to open door A. Now re-enter the main complex, but instead of going back to the transporter, enter the habitat section. Watch out though, as you'll be approached by aliens from all sides.
First, rid all the living quarters of aliens, then decend the stairway to the west. After using the recharger, head on through door A. Go to the large, circular room ahead and clear it of monsters. By the time you're finished, a secret door will have opened in the corridor you just passed through, leading to switch 2 (unlocks door B).
Go back just beyond door A and enter the group of small corridors, where you will find ammo, a comm terminal, and some monsters (make sure you find and kill them all). Leave the tunnels by door B, and jump across the gap into the centre chamber of the large circular room. Head down the stairs and flip switch 3 to open door C. Return to the habitat and head for door C before entering the heavily infested command and control center.
Get rid of the aliens, then ascend the steep stairway in the central area. Once you reach the top level, you'll be greeted by a bunch of Bobs (who are ever so glad to see you), a pattern buffer, and the final comm terminal. If you cannot transport out, some aliens must still be alive; the nearby switch will re-open the doors to the command centre so you can go back and check. But normally you'll be taken to level 4, The Roach Farm...
