This mission is a hard one if you want a silent assassin rating, but not too hard.
First, you'll need to gain access to the underground base. The topside map of the level is still easy to get through, the large distances and scattered guards make it easy to run through here unopposed. Also, if you want to sedate or strangle a guard for his disguise, this would be the easiest option for it. There are two points of entrance: The door closest to the starting point is locked but is easier to get into because there is only one guard who'll patrol away every now and again. This door will lead to a rather well-protected area though. The other door isn't locked but has a much more aggressive guard walking around, it will lead to the torture room.
Going to your target
Depending where you get in, there are two ways to get to the lieutenant (see map). If you went to the open door, you can kill/sedate the guard(s) beating up the civilian. He will tell you where the target is before running out of the bunker. Unless you killed all the guards above, he'll get shot but this won't harm your rating. Unfortunately the guards that frequently check on the prisoner will sound the alarm when they realise he is missing. You may also just sneak around this gruesome sight. If you took the locked door, you can go to your left where a single guard will be patrolling a hallway with a lot of cells that provide good cover. If you don't have a guard disguise yet, you'll have to sneak up on this guard because getting through the next hallway unseen is impossible. Be wary of the guard near the entrance though, there is a point in his patrol when he won't see you enter, but there are three other points from which he can spot you.
Note: It is possible to get into the sewage ditch without a guard disguise, this 'cover' is practically useless though. Guards will still see you and even be more alerted when the water splashes, and using the covers tends to be impossible when there is more than one guard around. Not to mention being limited in where you can get back up. I've tried, it is impossible to get to the target, the generator or the disguise in the barracks unseen through these. And sneaking up on a guard to strangle/sedate them from here seems impossible as well. As such, these ditches only seem useful to hide bodies in.
Go into the tunnel-like area if you want a M60 with ammunition, you can also get a different guard disguise here but this is pretty much impossible to get here in your suit so the purpose of it is beyond me.
Go to the target and kill him. There is a guard standing in front of the door, he'll move eventually. You can walk into the room and then sneak into the small sideroom. The target, too busy fawning over his hitman game collection, can easily be strangled as long as you crouch when opening the door. You can take the lieutenant outfit, but I found the guards to be more suspicious of you this way.
Securing the cargo
Head to the elevator and go up. The alarm that will sound will attract the guards but they won't shoot you. It might be a mechanic to prevent you from getting out of the elevator and taking a different route. It is impossible to avoid the alarm though, there are no options given to disable it, and turning off the generator will result in the door to the elevator not opening. This doesn't seem to matter, though.
When you get to the top floor, strangle or sedate all of the nearby guards to complete the mission. If you work fast, you can do this before entering the bunker as well even with aneasthetic. Note that while you can't enter the shed in the beginning, it will open from the outside once you went through it once. Also adding the M60 to your collection AND getting Silent Assassin is virtually impossible unless the two guards in question were dealt with before sending the cargo up.