As soon as you have control, climb out of the torpedo and get your Knife ready. Stay crouched for the majority of this chapter, using stealth to avoid having Commanders sound the alarm. In fact, you should see your first Signal Detected on-screen right away.
Move forward and carefully eliminate the two guards patrolling the ground level. One of them should walk right past you, making it simple. Head up the stairs to the next level, making sure not to let anyone spot you. This part is a bit more difficult, given there are two guards in addition to the Commander, but if you time it right, things should go smoothly.
When everyone is down, go through the only door you can. You should see a map on the right wall just as you enter. Grab it and continue along and through the next door.
This area is very cramped and full of four to five enemy soldiers. While you can definitely try stealth, we just whipped out the Automatic Shotgun and went crazy. No matter what option you go for, be sure to completely loot all of the sleeping quarters for an assortment of goodies.
Continue along the only path you can and through the next door. Head down the stairs and through one more door until you see a central area. Equip your Automatic Shotgun and hug the wall. As soon as the heavily armored soldiers approach, take them down and loot their bodies.
Take out the remaining bad guys and climb the ladder at the end of the hallway. You can only go in one direction, so follow the tunnel until you reach a thin piece of metal. Use your Laserkraftwerk to cut a path and drop to the ground floor.
The battle here is fairly intense, so don't be afraid to toss Hand Grenades and move around from room to room in search of health, ammo and armor. While things get slightly more difficult than normal, the Automatic Shotgun is a monster and will rip these guys apart without too much trouble at all.
When the last bad guy is down, and if you're not already on the ground level, head back there. You'll see an open door with a bit more opposition on the other side. Toss a few Hand Grenades to clear the road and then head on threw. Again, use your Laserkraftwerk to cut all the visible chains, then hook the radio up on the desk to complete this portion of the chapter.
Follow Set and Fergus but don't worry about any opposition; you should be home free from here on out. Just do as they say until you reach the secret vault, then run across the bridge and get ready to head up to the top. Use your Laserkraftwerk to shoot the hanging magnetic spheres, turning them into steps. Be careful to move quickly before the steps disappear. Just keep climbing and shooting until you reach the top, then lower and raise the platform as instructed to complete the chapter.