Note: there is an achievement/trophy 'Invisible Intruder' on offer during this mission for getting through the level without being spotted and without killing anyone. Fortunately the walkthrough below will provide you with a step-by-step process on how to do exactly that!
After getting out of the rail car, follow your friend along the tracks. Climb the wooden ramp on the right to find a lockbox containing ammo and +15 Military Grade Rounds . Drop down and check out the side area to the left behind the cobwebs for another lockbox with ammo. Ignore the tunnel to the right with the large door for now and continue to the dead end at the end. Approach your mate when he tells you to give him a lift for a short scene. Once he is up and away, turn around and duck behind the piece of cover nearby in front of the side door we walked past.
After a few moments, the door will open and two guards will emerge. Stay behind the cover here and wait for them to start patrolling away from you along the train tracks. As they walk off sneak up on them one at a time and take them down.
Work your way up to the open door and sneak inside and hang out in the shadows to the left as you enter. Look across the room to the right and wait for the guard on the lower level to patrol over to the door (he will stop at the nearby fire first and then move on). Take him out when he stands in the doorway. Return to the left side of the entrance and use the wooden crates here to climb up the short ramp here and drop down into the shadows on the ground at the end.
Hang out here for a second and wait for the guard standing in the light near the door of the room on the right (next to the iron bars) to patrol into the shadows near you and take him down. Enter the shadows next to the iron bars and face the door to the enclosed room.
There are 6 guards in here. The lower level has two rooms. The room on the right has a single guard sitting in a chair. The room on the left has a pair of enemies, one patrolling and one stationary. There are an additional 2 enemies upstairs.
Enter the door and look in the door to the left just inside. Wait for the patrolling guard to look away and then move over to the right and take out the guy in the chair. Sneak into the left hand room and take out the guy near the fireplace and then the patrolling guard (it is best to let the patrolling guard approach the stationary guard and then start walking away before you strike). Return to the first room and climb the stairs to the left.
At the top of the stairs stay in the shadows and wait for the guard to the right to patrol off. You will see a guard patrolling the walkway outside of the windows here. Wait until he stops in front of the door opposite the top of the stairs. As he starts to move off, sneak out after him and take him down. Return to the shadows at the top of the stairs and wait for the guard on the right to patrol into the room. Run over and take him down.
When you are clear here, look on the control panel near the windows for a Diary Note [Note 1/2]. There is also a Pistol on the crate nearby. Return downstairs and enter the left hand room. There is a door in here exiting to the room on the far side of the iron bars. Just to the right of the exit is an enemy sitting in a chair. As such, crouch and walk out the door and quickly enter the shadow to the right. Run up and punch him out.
Climb the stairs at the far end of the room all the way to the top and enter the door here. As you do, an enemy through the open door ahead will notice you and surrender. Run over and knock him out if you wish to do so. You will find another Diary Note [Note 2/2] on the table in here.
Exit the door to the left and in the next room walk past the light pointed at the open vent and on the ground nearby you will find a lockbox containing +5 Military Grade Rounds . Walk over to the open vent along the right hand wall.
You will earn an achievement/trophy and a Morality Point at this time if you made it through the level without being detected or killing any humans.
Note: For completing the mission without being detected, you will unlock Achievement/trophy ‘Invisible Intruder’.
Follow the vent until the screen blacks out to complete the mission.