1: After entering the Heron’s Loft area from Lower Seattle Slums, you’ll see a ladder on the far side. Approach it and continue around the corner to the door. Enter the apartment complex and take a right to see a broken elevator. Crawl underneath for a couple items, and enter the vent. Climb the vent and you’ll emerge in Gob-zilla’s room, with a female thug guard (who can sometimes unload a spider bot on you). If you have an unequipped 
Silencer, now would be a good time to install it on a weapon. From the vent, kill Gob-zilla and the female who comes in from the next room.
2: Search the room for items, including the apartment’s softkey, which is opposite Gob-zilla’s cage. Exit the room through its door, and continue down the hall to the next apartment, which happens to be the manager of Queequeg’s Coffee Shop. He’ll offer you a quest to approve his zoning application from the WTO enclave. Search the back room for the softkey to Queequeg’s Coffee Shop. Exit through the door down the hall and talk with the guard near the tall fence, who will give you permission to see Miss Sak upstairs.
3: Head back inside the apartments and back to the broken elevator. Inside the shaft is a ladder you can use to climb up to the top. Exit onto the top floor and you’ll see a couple guards patrolling, as well as a door down the hall with guards outside. Take a quick right after exiting from the shaft, and walk into the first room on your right, down the hall a ways. Close the door behind you and you’ll see four chests with items inside. The important one is the one across from the door by the window. Use a multitool to break in, and read the datacube for security codes, and a 
Refire Rate weapon mod.
4: Search the other chests if interested, and head back out into the hallway. Take a left now and another immediate left into the small entry way with security panel on the right wall. Use it with the codes you just found, and turn off the cameras. Now get back into the hallway, and turn right to get to Sak’s office at the end. Open the door and speak with her. For 250 credits, you can pay off Sid’s debt and hire him as your pilot. Or, you can choose to fight her and the guards.
5: Exit the office and head down the hallway opposite the broken elevator to the helipad area with guards. You now have permission to enter this area, so walk past the guards to the other side of the small area, and enter the helipad hangar through the entrance door. On the right side of the large room, walk up the ramp and use the security terminal to turn off all cameras. You can search the below-ground maze for a few useful items if you like, but the main attraction here is the weapon storage room high up on the left side of the hangar.
6: Use the ladder, cloak yourself to avoid getting caught by the guard picking the lock, and use your multitools to enter the door. Once inside, you have no need to continue cloaking, as long as the guard didn’t originally see you. Take all of the weapons you want plus 
Ammo Scavenger mod and a free recharge at the repairbot, before exiting.
7: Head back to the Lower Seattle Slums, until you are just above the large ramp in the alleyway. Ahead in a small alley is another Omar Trader. If you still have preferred privileges, you can buy his BLACK MARKET BIOMOD CANISTER for 500 credits, and pick up some energy cells for another 300. I was near the max (10) in energy cells by this point so would advise against it if you’re in the same boat. I’d strongly recommend upgrading 
Spy Drone to level 3, the maximum. You’ll really notice the energy drain and power difference and it can now make people unconscious as well.
8: Up from the Omar Trader is Queequeg’s Coffee Shop on the right side, and the entrance to the Order Church on the left. For now, let’s enter Queequeg’s with the softkey you got back in the manager’s office in Heron’s Loft. You can also enter via a vent above the dumpster outside. Destroy the beans using your preferred weapon (in my case, an energy sword from the Culture Minister’s Penthouse so as not to use up ammo). Your quest log will update, and you can now head across to the Order Church entrance.
9: Inside the Church, walk straight ahead and up a small set of stairs to talk with Her Holiness via holocomm on the pulpit. After that, head to the right side of the pulpit through a door and up some stairs to receive a message from Lin-May Chen on the holocom. She instructs you to find the Order traitor in named Lamar in the Inclinator Facility.
10: On the left side of the pulpit, enter the maintenance door and go down the stairs to an electrical area, where two spider bots patrol. Use your Spy Drone (or preferred method) to take them out, and walk around the left side to the back for a repair bot. The highlight of this room is the increased damage weapon mod under the floor. When you’re through here, head back out to Lower Seattle and back to the Inclinator Facility, and be ready for a fight.
11: Once inside, you’ll be behind a crate. On the other side are two Templar thugs you’ll need to take out or sneak past using 
Cloak. It’s up to you how to deal with them, but one method is your 
Biotox Attack Drone or boltcaster if you wish to play the pacifist. By now your Spy Drone can also knock people unconscious so you could perform a quick two attack on the thugs to knowck them out. Afterward, take the inclinator back up, but beware another Templar thug on the balcony to its right.
12: At the top of the inclinator lift, where the spill was, use the repair bot to charge your energy and head through the door on the opposite side. Continue down the hallway until you get to the stairs up. There are two more thugs here. Deal with them, and continue to the door to the director’s office, as before. If you want to settle this peacefully, use your cloak and simply read the datacube in the director’s office, then exit. If not, you’ll need to take care of Lamar and guard in the same room. After reading the cube, your quest will update and you’ll be asked to return to Lin-May Chen at the Church. You may as well do so now, and clear up the Gob-zilla quest while you’re at it.
13: At the Church, talk with Lin-May Chen who gives you your last quest here, which is to hire a pilot to fly you to Mako Ballistics. That would likely be Sid Black, but could also be Ava Johnson, as this walkthrough recommends. After the conversation, head back into the Greasel Pit Tavern, and tell Sid his jet is free. He’ll offer to be your pilot and says to meet him at the landing pad when ready.
14: Go back downstairs to the Greasel Pit arena, and bet all the money you can (500) on Snake-eyes. Watch the fight and collect your 1800 credit win. Talk with Eddie afterward for your 100 reward.
15: Time to go back to Upper Seattle, and to the Coffee Shop to collect your 300 credit reward. When that’s done, head upstairs and then to the right toward the Metro Station. We’re finally going to the WTO enclave.
