Make sure to look at the Passive Playstyle Character Build section to get an idea of what sort of weapons/items/augs work well here.
Note: I did all of Mako without the Thermal Masking mod.
It's much easier to do Mako on passive if you paid to free Sid Black - he deposits you on the roof nearest the entrance, where you can crawl across to the ventilation entrance that puts you in the conference room inside. If you used Ava instead, you might want to root around and pick up some loot, but you'll probably want to make your way to where Sid would drop you anyway. This will be tough, as there are Hunter/Seeker bots on the ground with the guards, cameras and turrets. Bonus points if you can do it without alerting anybody.
You will need an EMP-enabled weapon (preferably a silenced pistol) to disable the gas beams. An EMP nade will also work but may alert the guard.
Once you are inside the conference room, make sure to get the access code off the table. Watch the guard as he goes by, and time your exit from the conference room based on his patrol and on the camera to your left. Go to the right towards the main hallway. There's a ventilation duct here that takes you down to the service tunnels. Time your entrance to it based on the patrol bot's path. There's a spiderbot inside, which you'll have to disable. You can avoid this duct if you jump over the stair railing near the conference room, but you might trigger a camera doing that which makes the turrets active. Either way, whether you jump the railing or take the duct, you'll find yourself at the service tunnels.
In the closet nearby, hack the powerbox and shut off the power. Go into the service tunnels. At the entrance will be the other keycode. Get that, then head back to the staircase. Wait on the staircase for the patrol guard to slip by, then sneak over to the Advanced Weapons Lab. You should have the key, so open the door and go in. You may want to cloak just to make sure the guards don't spot you. Once inside the lab you are safe. Take the Mag Rail and head back out. Note that the two patrol guards will now be in the hallway coming your way... you will either need to be quick and go into the ducting to avoid them, resulting in a Spider Bot kill, or cloak past them. Note if you bump them or bump the boxes trying to move past them, they can still take shots at you when cloaked.
Now sneak back down the staircase into the service tunnels. There's only one guard down here, so sneak or cloak past him to the opposite end where the ladder takes you up to the Biolab. Wait for the patrol bot to head away, then go on in. You should have the key.
There is a turret and a patrol guard here, along with another guard inside a security room. It won't be easy getting past them without cloaking. Note that if you free the Grey, it will kill the guards - so avoid doing that. Due to the layout of the room, you're pretty much forced to cloak here - watch your energy meter. There is no camera, but there is a turret, and if the guard notices you, it will go hostile. Once you get into the back room, shut the door behind you and stay crouched - the guards outside won't pay attention to you anymore, though there is another guard in this room. Duck behind a pillar to get both him and the turret out of your line of sight. You'll be able to chat with the Project Director.
If you are careful you can also snag the biomod cannister without alerting the guard. Then move just past it to the ventilation duct. This leads to Dr. Nassif's office. There are gas beams inside the vent - your trusty mag rail will work, but a silenced pistol is a better choice so that the guards don't go on alert. The guard can see you through the glass in her office so make sure you sneak by when he's turned away. Now, you need to do a complete 180 and make it all the way back outside. You'll need to cloak past the guard again in the adjoining room. From there you'll be back at the ground floor.7
Ground Floor / Escape
Listen to the security bot so that you don't get surprise by it and head into the service tunnels. This time you can sneak past the guard without cloaking, heading to the left. There will now be more guards than before, so you will have to be sneakier than last time. Watch your meter when cloaking. There are 2 guards in between you and the roof. If you think you can do it, you can try to run past them - but I would suggest tossing up cloak and sneaking right past them.
Ava or Sid will be waiting and you are home free.
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