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1: This walkthrough flies with Ava Johnson, though if you chose Sid in Lower Seattle, simply skip ahead to the roof section at #3, as that is where you'll get dropped off. When you land, check the dumpsters and around the area, and ready your anti-spiderbot method of choice. To the north is a semi-hidden vent grate. Open it, disable the two spiderbots within and continue through these smaller tunnels to the grate at the end, making sure to notice the two multitools (on ledges) and energy cell on your way. When you open it, you'll emerge in a room with a man named the Groundskeeper.
2: Talk to him to be offered a key to the entrance for 250 credits. We'll be going through a roof vent so save your money. Exit the room through the door into a hall with a repairbot. If you have Spy Drone, open the main door to the left in the same hallway, hide in a niche, and prepare your Spy Drone for action.
Outside of the door we're going to take out 3 guards, one Hunter Seeker security bot, a camera just below ground level on the open lower level, and across the way where it says Cargo Bay, another guard in the hallway there - all while this repairbot keeps you refilled. After this is done, you'll be free to move around as you please, at least down here. If you don't have Spy Drone, simply use your weaponry to do the trick, and don't worry about the camera.
3: Head across to the Cargo Bay where the former guard was (or live guard if you didn't get to him yet). When the hallway is clear use a multitool to deactivate the green triad of lasers in the left niche with ladder behind. Climb the ladder and follow the linear path to the roof. When outside, climb the small ladder ahead and look west across a ledge to another camera and ground-mounted flame turret. Use your Spy Drone on the camera and mantle across the ledge to where the camera and turret were. There's a vent grate here against the building you'll use to enter the Mako Interior. You'll get commed a message congratulating you for finding an alternate entrance as you approach the grate. Open and enter.
4: When you emerge in a darkened room, read the datacube for the keycode to the Biolab. Donna Morgan will com you with instructions. On the other side of the door, there's a guard patrolling the area, and a camera on the left side. Use your Spy Drone (or other method) on the camera and guard, and then walk left out the door toward the camera and then right (west) up the hallway. There's another camera on the northwest end of this section. At the end of this hallway will be a scientist and another guard, either inside or outside the room named Guard Station at the end. Take him down and don't worry about the (likely) scared scientist. Take out the camera as well. Backtrack toward the first camera and take the stairs down to a large hallway and entrance labeled Service Tunnels.
5: Open the service tunnel door and descend the stairs. When you get to the first small room, read the datacube on the shelf to the right for the keycode to the weapons lab. Head back up the stairs now, and then again up the first set of stairs to the main hallway where you did the fighting. Take a right and notice the "Advanced Weapons Development" writing on the wall. Open the door.
6: Climb the ladder ahead and enter the door at the end of the hall. You'll enter conversation with the head scientist. If you want to help the Order, this is the one you'll want to kill. However, I chose to tell him you won't break the Mag Rail, and let him go upstairs. You can still side with the Order later. Use the switch on the Mag Rail case to open it, and then take the gun. It's actually a quite useful piece of weaponry, having an EMP alt-fire mode that destroys bots and the like. Donna Morgan will now congratulate you.
7: Head back out the way you can, but be on guard. At the nearby ladder down there will be two guards you need to deal with. Go back downstairs to the Service Tunnels where you recently picked up the keycode and prepare to fight another guard (somewhere in the vicinity). Open the grate on the floor and crawl to its destination. Jump out and ignore the door on your left. Instead, enter the room at the end of the hall - the one with a ladder leading up. Climb the ladder and you'll be in a small room next to the elevator to the Biolab.
8: Outside this room just to the right of the elevator straight ahead is a security bot patrolling the hallway that you can destroy with your Spy Drone or newly found Mag Rail using alt-fire. Or, you can simply ignore it and enter the elevator. Take the elevator to the Biolab and have a talk with the two scientists in the first room, but beware of the guard patrolling upstairs in the lab beyond.
9: You'll want to take out both the guard upstairs and the guard in the Guard Station, also upstairs, and who will exit as soon as you go hostile with the first guard. When the two are subdued, head downstairs and into the right hallway to check out the Gray. The datacube to release him is on a desk in the area. Now go to the Guard Station upstairs and read the datacube for the Director's Office keycode.
10: Enter through the only other door upstairs, which leads to the Director himself. Have a chat with him, but beware the guard just up the small set of stairs next to his actual office beyond. Take both the guard and turret out, heal at the medbot, and sally up to his office door. Open and enter, then view the holocomm message regarding Nassif. You'll be updated with a new goal of going back to the roof to meet your pilot, in this case, Ava. Before you do so, head back to where the director was and open the case to the BIOMOD CANISTER using your multitools.
11: Now it's just a simple matter of backtracking. There's a shortcut back to the roof, but it's only a little more dangerous; we'll take it. After you ride the elevator back, exit and deal with the security bot in the nearby hallway, if you haven't already. Follow that hallway all the way, go up a set of stairs, and keep left until you slip into the room you first entered from the roof. Take the vent back to the roof, and then Ava's Jet to Cairo.
