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1: The way to the WTO terminal is through the metro station, which is up the stairs in Upper Seattle. When you nearly reach the apex of the stairs, you'll see a vent on the wall straight ahead. This is a more cost effective way, though aggressive, of getting through the lasers that prevent you from using the metro. You could also simply pay 250 to the "cashier" who's at the booth ahead.
2: Enter through the vent and you'll emerge at a hallway behind the cashier booth, where a guard also patrols. The easiest way of doing this is to turn on your Cloak, enter the cashier booth, flip the switch on the right side of the booth that disarms the lasers to the metro, and hightail it out of the hallway into the metro, making sure to stop and open the locker on the right side of the hallway on your way. All cloaked. Just stay to the right and you'll find your way out of the small area.
Another method would be to take out the guards in the halls and booth, flip the booth switch and take your time. That's up to you. I chose the stealth method. By the way, once you disarm the lasers and re-enter the metro station, all unseen, the guards are friendly to you again as they should be.
3: Enter the metro and take it to the WTO, where you'll find yourself in a rather large lobby. Ava Johnson will com you that she's being held in the hangar below. Head straight and right around a wall, into an office section. Next to the right window is Klara Sparks, your fellow Tarsus Academy student, who's worked fast to land a job here. She'll have a quick conversation with you. Across the hall is the entrance to the Civic Manager's office and Donna Morgan. Head left into Donna Morgan's office now and speak with her on the holocom. Your new mission is to hire a pilot and fly to the Mako Ballistics, just like with the Church.
4: Now exit her office and go to the Civic Manager's door across the hall. You'll hear him in conversation, and he'll exit the room afterwards. Now is your time to sneak past him into his office. Check the second locker from the left for a silencer weapon mod. Use a multitool on the wall safe to find a datacube holding his login for the terminal in the room. Use the terminal to approve Queequeg's Zoning Application. On the way out of the office, talk to the Civic Manager himself and you'll be rewarded for your financial detective work in the Club Vox Owner's office.
5: Since you've approved the zoning application for Queequeg's manager, you can go back to see him for a 300 credit reward, and then return here for Ava's resuce if you like. You can also accept Sid Black as your pilot right now and head to the roof of Heron's Loft where he and his jet await. It will cost you 500 credits for the trip but you'll end up slightly closer to your goal once there - on the roof. When you rescue Ava Johnson, it's free but you'll be a little further from your goal when you arrive - on the ground where you must get to the roof. In my opinion, Ava's route is the better deal, plus you get to see more of the game.
6: If you decide to stay and rescue Ava Johnson, head to the elevator in the WTO terminal with a guard on either side. Enter the elevator and head down to the terminal. You'll find yourself in a room with a door ahead. Beyond the door is the terminal, and some guards and security bots. If you've got Spy Drone at level 3, this part of the game is going to be very easy. Even if not, it's not very difficult, though whether you choose to kill or simply knock unconscious will be up to you.
7: Ava Johnson coms you your goals: disable the ground-to-air missile batteries, one on either side, and then flip the pilot beacon on within the control room. At that point, you can leave. Sounds simple enough? It actually is. What are the ground-to-air missile batteries? They are huge missile turrets planted on either side of the plane, which is straight ahead as you enter. The easiest way to take them out is the Spy Drone's EMP attack but if you lack that, there are security codes and a maintenance key you can find for an easy alternative, which will be covered at #10.
8: Enter the door, and head left. Beyond the crate will be a couple of guards. Cloak and slip past them and look for a nearby door on the right side wall, against the platform in the center of the hangar. It's unlocked, so when you enter, take an immediate left and notice the first door to your right, just before a set of 3 lasers. Use your mulitool to enter the room with a repairbot and some items. Decloak. The repair bot is the essential thing here, as it will continually keep your Spy Drone fully charged, and you can defeat most all obstacles from this room.
9: First use your Spy Drone to take out the two guards you passed earlier. Now for the missile batteries. Exit the door that leads to the two now unconscious guards, and head right (west) with your drone. Take out the security bot patrolling the area with the southern missile battery. Now use your drone to take out the missile battery itself. Should take two attacks. Now use your drone to go around to the other side and take out the security bot, the camera and the northern missile battery. Just for good measure, you may wish to take out the turret just outside this room beyond the lasers.
10: Re-cloak, exit the room and head outside to where you first saw the two guards, and descend the pit with the ladder leading down. There is also another similar one on the other side. Another guard will be down here somewhere, perhaps up the corridor. To your left when you enter, you'll see a laser grid to your left. First deal with the guard and decloak, then head left until you get to a small alcove with a machine on the right side. To the right of the machine on the ground is a datacube holding the security codes for disabling the missile batteries if you haven't yet already done so.
11: There is no reason to pass the laser grid because there's another entrance to the west and nothing else to do here anyway. Head back up the same southern ladder you used to come down and enter the south Control Room door. In the control room is a locked chest with an increased damage weapon mod. Before you flip on the beacon (if the missile batteries are disabled already), enter the vent in the control room. It leads to another small maintenance room with security terminal, and a softkey to the maintenance door right by the barrel on the ground. Pick this up if you haven't disabled the turrets. Use the security terminal and disable the south missile battery. One to go if you haven't done so. On the other side, there's another maintenance door that you can open, and a security terminal in the room where you can disable the northern battery.
12: Head back to the control room and activate the pilot beacon. WTO guards will rush in, so activate your cloak, exit through the door and head up the center platform to the helicopter. Ava will now take you to the Mako Ballistics facility.
