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After climbing the ladder and opening the door, you will encounter the Pit worm. It is a large enemy that needs to be destroyed, but won't fall to your small weapons. It will swing at you, as well as shoot an eye beam.
Jump down, and turn to the right. This brings you to a set of broken stairs with two pit drones, and a vent underneath the broken staircase. Enter the vent, and you should reach the control room. The control room shows what's needed to kill the pit worm, but it needs a valve and gearbox to be active. You may activate them in either order.
The valve is within the main lair. Take the right-hand exit from the control room, and climb the ladder. You should reach a switch that activates the vent.
Switch to the barnicle, and pull yourself to the platform on the other side. Activate the valve, and head for cover.
The gearbox is found in a side area.
From the control room, take the left door and walk across the walkway. You'll reach an airlock, which you will pass through. There won't be much combat in this area, but there are still a few pit drones.
After the airlock, kill the first drone, and climb down the ladder. Enter the door, and you will see several boxes blocking your way. Jump onto a small metal box, to climb over the large one. Turn left, and jump over the spill. Head up the lift and enter the control room. Defeat the two pit drones and press the button to start the compactor.
Return to the compactor room, and break open the floor vent. Jump in, break the side glass, and enter the room. Turn on the gearbox and return to the shaft before the chamber floods. The rising water will let you return to the main lair.
Return to the control room. Press the button, and the pit worm will be hit with toxic waste. Return to the bridge control, either by returning through the vent, or the faster route by heading right and jumping onto catwalk below the controls.
Press the button on the controls, to extend the bridge. Crossing the bridge will bring you to the next chapter.