Work your way along through the wreckage. Atlas will ask you to hit a switch so make your way towards it. Smash the padlock on the gate when you reach it and turn left to find the control panel. When you activate the control panel you’ll be locked in the booth.
You’ll see Atlas down below as he scurries through the door and works on a panel oblivious to the threat above. There is nothing you can do here so just watch what happens. After the attack, you’ll find the door to your left has opened.
Grab the explosive cylinder and turn left into the corridor using it to blast away a Splicer. There is a medical station on your left and then a Splicer to your left and one straight ahead. You can set the area to the left on fire. As you come down a series of wooden walkways you’ll be attacked by another two Splicers as you turn left towards the submarine.
On your right you’ll pass a locked gate, smash the padlock to go inside and grab some extra pick ups, an audio log and some cash. You’ll also find another exploding cylinder which you can pick up with Telekinesis and fire at the next Splicer back in the corridor. When you reach the submarine, it will explode dramatically. Search for pick ups scattered around here on corpses and then continue to follow the arrow. It will lead you to the bulkhead door and you have completed this level.