1. Directly across from Queequeg's is the Order church. Use the indicated keypad to open the doors, then pass through another door on the right (inset).
2. Approach this holocom unit to converse with Her Holiness. She instructs you to receive a message from Lin May Chen in the next room.
3. As long as you don't mind stealing from church, swipe these two credit chits worth 125 credits from behind the pulpit. Phosphorus flares and a boltcaster can be found beneath the platform.
4. Continue through this door and ascend the stairs.
5. Approach the holocom and receive a new goal from Lin May Chen: find the Order traitor Captain Lamar in the inclinator. Grab the ammo clip from the table.
6. Inside this locked chest you'll find a spider bomb, 100 credits, a scrambler prox mine, and a noisemaker grenade.
7. Backtrack past Her Holiness and open this maintenance door.
8. Before descending the stairs, send your spy drone down and disable the two spiders on patrol.
9. Multitools on this power box will stop the arcing, but you can easily get around the other side if you prefer.
10. Grab this energy cell. There's also a concussion prox mine on the floor nearby (inset).
11. Approach this medbot on the far side of the room to heal. Note the ammo clip on the floor to the left, and the EMP grenade to the right.
12. Under the subfloor is this increased damage mod, a multitool and an ammo clip.
13. Backtrack to the inclinator. Three Templar recruits patrol the area and are hostile. Activate your cloak or use your biotox drone to subdue them.
14. Ride the inclinator to upper seattle. Lin May Chen spots Captain Lamar and the Templar fugitive in this office, completing the objective. You receive a new goal: find evidence.
15. More Templars are in this part of the facility. Activate your cloak and head to the facility director's office.
16. Even though you are cloaked, you will trigger a cutscene if you approach the Order Captain or the Templar. Not to worry, as they will be unable to see you once the scene ends.
17. This datacube is what you're here for. Read it to complete the objective. Lin May Chen instructs you to return to the Order church.
18. Don't forget about the facility's repairbot. Use it to recharge and keep your cloak active. One technique I found to be useful was to remain cloaked and activate the biotox attack drone, returning here to recharge. You can easily wipe out the resistance in the inclinator this way.
19. Return to the Order church and talk to Lin May Chen. She instructs you to hire a pilot and fly to Mako Ballistics.
20. Before leaving the church, Billie Adams interrupts for a brief conversation.
21. Return to Sid Black at the Greasel Pit. He'll instruct you to meet him at the landing pad when you're ready to fly.
22. Head downstairs and approach the bookie. He lets you know that Gob-zilla has been killed (he doesn't know that it was you), but you can still place your bet. I recommend putting 500 credits on Snake-eyes.
23. Walk over to the railing and watch the fight. Snake-eyes usually defeats the Claw. Return to the bookie to collect 1800 credits.
24. Return to Eddie and collect your 100 credits for killing Gob-zilla.
25. Exit the bar and take the inclinator back to the Upper Seattle City Center. If you didn't resolve the situation with the thugs earlier, you'll have to now. The dialogue options are the same, except you no longer have the option to run to the ATM.
26. Return to the Pequod's coffee shop and collect your 300 credits for destroying the Queequeg's beans.
27. Follow the signs to the Metro station.
28. Talk to the nervous attendant and learn that the prices have increased five fold. You can either pay the 250 credits to have him disable the gold security beams (inset), or you can sneak in.
29. Here is the convenient air vent. Open it and climb through.
30. Activate your cloak and pass through the door to the attendant's room. Activate the indicated switch to disable the security beams.
31. You'll find an ammo clip on this chair behind the door.
32. In the neighboring storage room you'll find a medkit, an ammo clip, and this dead body. If you talk to the nervous attendant again you'll have the dialogue option to tell him about the body. Not a great idea, as he'll start shooting at you.
33. In the hallway is this unlocked locker with the key to the nearby door, a stun prod and an ammo clip.
34. Use the key to open this door and pass through the now-disabled security beams. Ascend the stairs and press the switch to travel to the WTO air terminal (inset).
35. Ava Johnson tells you she is in the hangar on the lower level. Talk to the WTO Captain visible directly ahead and he encourages you to join the WTO. Ascend the stairs and keep right.
36. Approach the window on the right and talk to your old school chum Klara Sparks. She's now working for the WTO.
37. Head to the management wing across the way and hang a left into Donna Morgan's office. Approach the holocom to talk with her. She wants you to find a pilot and fly to the Mako lab north of town.
38. Grab the multitool on the floor under the desk. On the coffee table is this book with some background on the Dentons. The book faults them for the collapse but at least gives JC credit for resolving the Gray Death.
39. Wait for the civic manager to come out of his office, then approach him to collect your reward for spying on the Club Vox owner's finances.
40. Enter the civic manager's office (the door was locked previously). The left two lockers are locked. The first holds two ammo clips and the second holds a silencer mod. The right two lockers are unlocked. The third is empty and the fourth holds some food.
41. Inside this safe is the civic manager's login, a scrambler grenade, and an EMP grenade.
42. The login allows you to accept the zoning application that the QueeQueg's manager wants.
43. Ignore the nearby elevator for now. Instead explore the Pequod's and the surrounding air terminal. Check out the view and you can see Anna's helicopter below.
44. Return all the way back to the Heron's Loft in lower seattle and receive your compensation from the Queequeg's manager for fixing his zoning application.
45. You've now got a decision to make. Who do you want as your pilot? If you choose Sid Black, head to the roof and you can leave now. Sid drops you off closer to the action, but it'll cost you 500 credits. Personally, I want to see the entire map so I think this is a bad gameplay device.
46. If you prefer Ava Johnson, backtrack to the elevator in the WTO air terminal we bypassed earlier. Rescuing Ava will cost you some standing with the WTO (not that it matters) She will land in a different spot at Mako than Sid, but I don't think it's any worse, and she will not charge you for the trip.
47. Ride the elevator down and approach the terminal door ahead. Ava instructs you to disable the ground-to-air missile batteries and activate the pilot beacon.
48. Activate your cloak and bypass these WTO guards. Slip through the unlocked door on the right (inset).
49. Make a left then use multitools to open this door on the right.
50. Inside is this chest holding a black market biomod canister and a spider bomb. On the floor to the right is a concussion grenade and a medkit is on the opposite side of the room.
51. What's really critical about this location is the presence of a repairbot. The combination of cloak, repairbot and your level 3 spy drone will allow you to secure the area from the safety of this one room.
52. Use your level 3 spy drone to knock the two WTO guards unconscious. The repair bot will recharge your systems as they are deplenished.
53. Your spy drone's EMP blast will take out this security bot and the south missile battery with ease.
54. Repeat on the other corner of the building by taking out another security bot, the north missile battery, and the security camera seen in the background.
55. Lastly, send your drone down one of these openings to the lower level. Do this quickly as your spy drone will deactivate if over its maximum height for long.
56. Knock unconscious the lone WTO soldier patrolling down here. The area is now secure.
57. Deactivate your cloak. Head below (where you last sent your spy drone) and read this data cube to obtain the security login codes. The security guard you knocked out earlier has dropped a shotgun and a concussion grenade. The unconscious guards above have dropped a spider bomb, a boltcaster, a pistol, an EMP grenade, and ammo.
58. Don't waste a multitool on these lasers. Another access ladder is available on the other side.
59. Grab this multitool.
60. An alternative method for disabling the north missile battery is to access this maintenance room. Use the security login to access the security computer and deactivate the missile battery (inset). The only other items of note in this room are two ammo clips, a medkit and a data cube revealing the presence of the black market biomod, so save your multitool if you've already disabled the missiles.
61. Time to enter the control tower.
62. Slip through this vent. Grab the multitool before exiting out the other side.
63. This is the south maintenance room. An alternate method to deactivate the south missile battery is to use the security login on this computer. The softkey to the maintenance door is on the floor to the left of the vent.
64. Shimmy back through the vent to the control tower, where you'll find this locked chest holding an increased damage mod.
65. Here's the pilot beacon (a picture is on a data cube to the right). Activate it and Ava radios that you're ready to go.
66. More soldiers now patrol the area. Activate your cloak or prepare for a fight. The control tower makes for a good sniping location. Board the chopper and Ava will drop you off near Mako Ballistics -- a bit further away than Sid's harrier will take you.