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NOTE: I'm sure that I missed a few routes. There are a ton of paths that you can take in an incredible amount of combinations. The following are just the ones that I found to be fairly practical and available to the average player. If you have a better/more fun route, feel free to use the comments below to discuss it.
Also note that you really need to throw a few points into upgrading your skin's armor rating at least once. You should receive a few praxis points during the mission (it's fairly long), so keep that in mind when upgrading.
In this outer area, you can find a MCB gang leader who is surprisingly nice. He'll act as a good arms merchant in this region, so feel free to buy some extra gear, mods or ammo if you need anything. He'll be here until the end, if you need him.
When you're ready, go through the doors and continue moving forward until you spot the mercenaries and the FEMA soldiers. I suggest that you make a save point here, at least as a permanent fallback point. When you're ready, go on out to face the first set of patrols.
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Getting Inside the Facility
There are six guards out here. There are three on the left and three on the right. If you wait for them to split up, you should be able to do a takedown on the first guard to the left and then chain up the takedowns to clear the left side. Put a tranquilizer round into the door guard and the way is basically clear.
A slightly better option is going to the right. Take out the first guard to the left now and hide the body by the shack, then cut to the right. If you hurry, you should be able to make it to the lone guard standing behind the truck. If you take him down here, you won't be spotted. If you look at the office to the right, you should see some well placed crates. Just grab a box and drop it on the ground to climb up and go through the window. Loot the room and open the door to come out right behind the guard. Take him down, and shoot the guard on the raised ramp with a tranquilizer.
Move back to the left and you can easily take out the stragglers.
Now that the yard is clear, we can carefully consider our path.
There's one that goes around the back, but it seems a little needlessly complicated. There's also a rooftop path. The front door is also open, but you really don't want to end up on the first floor. It's a bit of a killing field.
The best way is to hack the keypad on the gate to the left of the front door. If you let Sanders go, then you already have the code. You learn that 7984 will unlock most of the keypads, and "Neuralhub" will unlock security terminals. Regardless, it isn't a terribly difficult hack. Open this up and climb the ladder to find a route into the main room and you'll wind up on the second floor.
If you can't get in through this route, try going in through the front door and then use the crates as cover to get to a ladder and make it to the upper level. It's a really good spot.
Once you're on the upper level, you just need to watch out for a sniper. He's directly across from you. Just stay low and walk toward him. It's fairly easy to just wait for him to start a patrol and quietly take him down. You can also grab the gun if you want. It's big though, and it won't do a whole lot in this area.
The real treat is right next to the sniper's perch. If you look by the sniper, you should find a vent that you can go in, which will put you out right next to the elevator that you need to take. If you use the vent on the second floor, you will easily be able to slip behind the elevator guard, hit the button and then go down to the holding cells.
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The Big Robot
This new area is a little complicated, but straightforward conceptually. If you didn't notice it, there are two guards on the floor, two on the second floor with a good view of the area and a really big robot with a minigun (it's hard to miss).
If you plan to fight the robot, then you'll want to grab the EMP grenade that's helpfully sitting on a crate by the elevator. There is also a rocket launcher in the room to the left, but you'll need to either climb over the barrier or sneak around to get it, because the entrance closest to you is blocked.
One EMP will kill the robot and make it explode and cause a lot of collateral damage, so if you want to fight it you should probably start with that and then just clean up the survivors.
There should be a few vents and grates that let you slip under the floor. The best way I found was to grab a crate from the stack to the left and then use that to climb over the barrier and get in the room to the left. Then, just walk forward and watch the guard by the clear door. He can easily spot you, so wait for him to turn his back and then move to the pillar by him. While he's on a separate part of his patrol, there should be a point when the robot and its handler turn their backs to you. Don't fight anyone. Just go through the doors behind you and keep moving.
Once you're clear, you'll need to stop and listen to two guards. They'll eventually split, with the second guard moving far down the line. Wait at the corner, and take down the closest guard. You can just leave him here, if you quickly move up and catch the other guard walking away.
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The Holding Cells
If you want to take the high road, just climb up the ladder. On this level, you can find a small armory if you want. Just hack the computer and open the door. You'll find a few rockets and some typhoon ammo, but you'll need to hug the wall to keep the camera from seeing you.
The main focus is the door out to the command center on the upper floor. I don't think that I'd bother hacking the computer here just yet, because it's possible to be spotted by a floor patrol. Don't go to the left. There's a camera watching the door and it's a pain to sneak out. Move the cardboard boxes and expose the door to the right. Go out and carefully swing out and try to do a takedown on the nearest guard. You'll then want to look around and use a tranquilizer dart, or quickly sneak around to do a second quiet takedown. The patrols overlap fairly well, so you'll need to keep the area clear to prevent alarms. Once the upper guards are down, you're fairly safe.
Just go across the floor and slip past the camera to reach the door, then hack the pad and go through (again, 7984 will get you through). There's also a ladder here that will take you down to another locked door. It doesn't matter which one you go through. All roads lead to Rome for this one.
The lower floor is harder to sneak through, but it offers a new option. If you know how to hack turrets, you can hack the computer right before you enter the big room (neuralhub will get you in) and flip the IFF codes for the turret. You can then just sit back and watch as it proceeds to kill everyone in the room and destroy all of the cameras. You can then waltz through. Note that this isn't exactly quiet, and you will be blamed for the deaths, so it won't work for a non-lethal run.
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The Medical Bay
You'll quickly pass through the medical bay. If you came through the higher door, you just have to walk down some steps to get here. They join up right before a large open area. Note the two men in the back left room. They have a great view of the area, are very quick to raise an alarm, and they both have revolvers. Since there isn't a lot worth looting around here, I suggest that you just stick to the main path while crouching and ignore them.
Your goal is the elevator in back. Hit the button, wait for it to take you down to the mercenary and then move through the empty warehouse until you reach a marked door. Go ahead and make a permanent save after reloading any gun that you want to use, just to be completely safe (the game should auto-save, but it's not fun to keep reloading your guns after every death)
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Boss Fight: Barrett
When you're ready, use the door to trigger a cutscene. Remember that you can skip this with “Spacebar." As you may note from my tone, I expect you to die a few times. That's just a fact, unless you're really good at avoiding gunfire, or you have a few upgrades into dermal armor.
I'll just start by covering what worked for me. You can stun Barrett quite well with an EMP grenade. In this time, it's possible to hit him in the face and neck with a shotgun for a full eight blasts (any gun will work, but a shotgun has a nice punch and times up well). You can then just run to the room in the front left and wait a moment. If you're lucky, his grenade throws will ricochet and just damage him. As he rounds the corner to face you, set off a nearby gas canister or explosive barrel to stun him again, and quickly unload the shotgun into him again. If you're lucky, this will be enough to kill him. If not, run to the right of him and just focus on giving him a wide berth and escaping to repeat this trick with the other room in back.
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Barrett has a minigun that can fire constantly with only brief breaks for reloading. He will usually advance while firing, unless you're knocking him back with gunfire. If he reaches you, or if you ever run too close to him, he will grab you and cause a ton of damage with a single hit, then try and shoot you in the face. Hit some buttons to break off and get behind some cover to avoid being finished off.
He can also toss grenades, usually three at a time. Frag grenades do a ton of damage, so get out of the blast radius.
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Tactics for Killing Barrett
The focus for this battle will be evasion. You need to sprint a lot and stay behind cover. Note that most of the cover will let you just bound from cover to cover and therefore move around the room without exposing yourself to machine gun first. From the barrier at the start of the fight, you can swing around to the right and go all the way around with a series of rolls.
Barrett can not be taken down in a non-lethal way. Boss fights in Deus Ex: Human Revolution do not count for the relevant achievement. The stun gun is somewhat useful, since it will always stun him briefly, but your focus should be on heavier weapons.
The room to the front left and back right both have many items in them. This includes weapons, ammo, typhoon ammo, an EMP grenade and some painkillers and energy bars. Look in here if you're feeling under supplied.
The best bet seems to be grenades. Grenades will stun Barrett easily and let you do a lot of damage. Concussion grenades work well, but they will blind you without the relevant augmentation. In this case, just make sure that you aim for Barrett before the flash. He'll stand still, so you can fire blind and just correct for recoil and be fine. EMP grenades avoid this issue nicely, and one should be in the back right supply closet.
Barrels and gas canisters will also stun Barrett, so they'll do in a pinch if you don't have any grenades and are having trouble getting into the side rooms.
And finally, note that it is possible to confuse Barrett. If you run around or roll behind cover a lot, it is possible to make him lose your trail briefly. This comes in handy if you need time to set up a trap or get some supplies from the side rooms. Just keep an eye on him, since he will find you after a short delay.
Other than that, you should be able to take him out with a few tries as long as you stay mobile and toss a few grenades. Once you kill him, just loot anything that's left in the rooms and then take the elevator out. You can then jump into the helicopter to go back to Detroit.
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Finishing Business in Detroit
Once you're here, you should stop and talk to Pritchard first. He'll tell you about a backdoor that Sariff put into the firewall, which is something that you should confront him about. Take the staff elevator up and talk to him. If you have the social module, you will be able to use pheromones and “Appease" to make him cooperate. Otherwise, pick “Refocus, Defend, Refocus, Defend" to win him over and get him to hand over some extra files on your unusual background. You can read these on the computer in your office on the third floor.
Talk to him again to debrief him on the situation and get your orders to go to Hengsha.
As the prompt will warn, this is fairly permanent. We'll be back, but not for a while, and any outstanding side quests will fail once you leave. I suggest (if you're following my guide) that you finish up Cloak and Dagger and then pay the merchants a visit. When you're ready, walk out to the helipad and talk to Malik to fly out to the new city.
- All information and screenshots from Deus Ex: Human Revolution