I originally was on a guide and wanted to put my experience there, but there is a 1,000 character limit. So here I will just copy and paste what I wanted to say over there, but be more detailed.


This is on the hardest difficulty - Masochist,(Yes, I play Hotline Miami, how can you tell?) you may not need to do this as this is a completely silent run. So if you aren't ever detected, you can get guaranteed one-shot kills.

Loadout
Tranq Rifle
Mk23 Supp
Taser
HSF-EMP
Empty Magazine
No Armor


Process
I will explain in minimal and as best as possible.

---Rush towards the first building - enter through the Eastern door and blast the man with your pistol.
Exit West of the room and keep running to the top edge of the Western wall, left. A patrol is upwards, coming from the left as well. Shoot him. This will alert the enemy inside this building.
Then, rush behind the door of the building you're beside. Wait for the enemy to open the door and after he exits with his back turned. Shoot him. This will alert a patrol nearby.
---Quickly make your way inside this building and wait for him to open the Southern door. Have your Taser out and shoot him.
Now you can slow down. Wait for the enemy left of you to enter the Southern room of this new building. Once he is inside, jump over the half wall and wait for him outside the door. Once he opens the door, shoot him with the Mk23 again.
Back to being nimble - this will alert the enemy in the restroom above. Quickly rush to the outside of his door and wait. Then shoot him. Again, alerting another enemy.
---For this last enemy in this building, rush to the door of the room he is in and block it once as he tries to open it. Then step back and as it's being bashed open, shoot him. Then shut off the light in that room.
Exiting the building through the Western door, carefully run North, hugging the wall to your right. Take out the two enemies conversing. Keep their backs facing you and watch out for the windows to your left.
You will then run to your left above this next building. Position yourself above the center of the building at the very top of the alley and wait for a patrol to come by. When the shot is accurate enough, shoot him.
---Now run to the left and you'll see an enemy looking over a half wall. Run past and shoot him. Continue South till you hit a breaker box attached to this building. Begin to pick the lock - do not shut off the lights yet.
Run back up till you reach the Western door. There should soon be a guard that will just stand behind the door and look downwards into the hallway. Open the door and shoot him.
Now rush back to that breaker box and turn off the lights. Run back to that door you recently opened and go inside. You will see two enemies that go to a light switch in the Southern room. Afterwards, they go to the breaker box. Once both of their backs are turned, you can open the Southern door and trail them to shoot both enemies at once - from the darkness.
---After those two have been dealt with, go back to that door you entered to get in this room. Then you will see two enemies sitting down and talking. Open the door to that room and swiftly shoot them both.
Now, quickly run out of the building through the East and run back into the building to your right. Keep going till you reach that half wall you previously climbed. Climb over it again and run downwards. There you will be able to see an enemy walking to the left of the building. Shoot him.
Notice nearby there is another enemy. He will stop at a certain point and turn his back towards you. I prefer to shoot him with the Tranq rifle, though you could use the Mk23 instead.
---Carefully make your way Southwest. There will be a new building where you will see an enemy sitting down and a convenient half wall nearby. Go to the half wall and use your taser on the enemy sitting down. Then climb over the half wall and wait.
If you haven't already noticed, there is one enemy in this building that patrols. Wait for him to leave the hallway and go there. Quickly shut off all the lights and wait inside the left restroom with the door closed. He will come back and want to turn the lights back on. This is when you open the door and shoot him with the Mk23.
This last enemy will not move, allowing you to carefully get close to him and shoot.
Exit the building through the half wall directly in front of you and slowly make your way South. Watch for a flash light. When you see it heading your way, back up and wait. This enemy will patrol to the right of this building. Wait till his back is turned towards you and shoot him with the Tranq.
---Continue South till you see a building to your right. Go inside and begin to pick the lock to the door directly South after entering. Keep your reticle low, to view the campfire down South. When you see a shadow appear, make your way towards the campfire slowly. That is an enemy. Wait for him to turn around and then shoot him with the Mk23.
Keep in mind that room you unlocked has +2 Tranquilizer darts and +4 Taser charges. For now, continue South till you reach a door with an enemy facing North inside. Beware of the enemy outside the building patrolling left and right. He is hard to see in the dark. When his back is turned, use your Tranq rifle to take him out.
Next, you will pick the lock and open the door with the 2 - 3 enemies inside and Taser the closest one. This will not alert the others.
---Position yourself by the door and get a clear shot on the enemy that comes in and out of the room to the Northeast. Use your Tranq rifle on him.
For the last enemy, carefully walk close and secure a shot with your Mk23. This building is clear.
From here, I'd suggest to stick to the far Southern parts of the map and slowly and quietly pick off the guards patrolling about. Good luck.

Unfortunately that is all I have for a step-by-step type of guide. It is generally what I did when I got the achievement. Somethings might be a little different depending on how fast or slow you are going. So from here, there isn't much that I can guarantee will happen - best to leave it here and have you decide. Of course, you could also make a save after all this. It too me a long time to get the timing right, but once I got past that point. I was able to do it no problem.


Notes
1. The beginning is very easy to replicate after a few times. Sooner or later you will be going through this portion with ease. Just don't be discouraged and become impatient or stray too much from a plan that works for you. Or else you will constantly fail.

2. If you have the opportunity to wait behind a door and jam it on an enemy, I would highly recommend doing it. If you have ever bashed a door open, you'll know that there is a few milliseconds where you are completely vulnerable because you are locked in an animation. The same happens to the AI. It is a guaranteed easy kill if you do this. Of course, make sure your surroundings are clear - as to not alert any other enemies. Or use it to your advantage.

3. When playing through this level, I kept my speed at a constant 3/5. I was able to get very close to many enemies and walk from behind walls and doors just fine-- though even running didn't seem to alert them. Never had a moment where my movement cost me a run.

4. Don't forget that the Tranq rifle is very accurate and great for targets that are far away, patrolling or going to move away from other enemies shortly. This will allow you to plan accordingly.

5. Night vision is very helpful and when inside of a completely dark room, enemies will have a very hard time seeing you, allowing you to get the drop on them. Keep in mind the amount of noise your movement makes. Don't get too close, but close enough.

Original comment on guide I wanted to leave.
YES! I did it. 100% accuracy. I used the Tranq rifle, Mk23 Supp, Taser, Hsf-Emp and Empty Magazine.

The start of the Repurposed Factory is easy to get through and with enough practice, the very beginning - you will never mess up.
The challenges come from the patrol around the outskirts of buildings, but if you're patient (unlike me) you'll have no problem. Also the more condensed areas with lots of activity can be difficult-- luckily there are a lot of patrols, allowing plenty of wiggle room to get those shots.

I used the Tranq rifle a lot because of the great accuracy it has - making long shots a guarantee on stationary targets - as well as the Taser for those condensed areas so no enemies in range could hear the shot. Also, the map has this one room that has surplus Taser and Tranq ammo. So you could get a majority of those 40 shots using the most silent weapons and if a tranquilized enemy is woken up by another - you can get double the shots.
I did also notice some 9x19 mm SS ammo thrown about on tables, so perhaps you could ditch the Mk23 Supp if you wanted. Though having that fast fire rate helps a lot with the bundled enemies.

Overall, this took a long time and I would highly suggest the Repurposed Factory because of that ammo room. Obviously, this is going completely silent. It took me a while, but I have the achievement.
Also, I did this in one single play-- every time I missed a shot, I'd just restart the level in fear of the game keeping track of my missed shots-- if I ever missed any when I load a save. Though on Masochist, you only get one save anyway.
Played around with the Hsf-Emp as well and didn't count as shots, so that's nice. I only used the Empty Magazine once and it was with the last enemy guarding the door to the main objective. I was still scared anyway, so I just rushed him with the Mk23.

Good luck to those who go for this achievement. It was the hardest for me.