You should see a map on the right wall just as you enter. When everyone is down, go through the only door you can. 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. Head up the stairs to the next level, making sure not to let anyone spot you. One of them should walk right past you, making it simple. Move forward and carefully eliminate the two guards patrolling the ground level. In fact, you should see your first Signal Detected on-screen right away.
Stay crouched for the majority of this chapter, using stealth to avoid having Commanders sound the alarm. As soon as you have control, climb out of the torpedo and get your Knife ready.