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1: If you flew with Ava (as the walkthrough does), you'll be dropped off in Trier Square, marked on the map. She'll let you know shortly that the Nine Worlds Tavern would be a good place to start looking for clues. Talk to the nearby citizen to learn something has happened to Her Holiness, and then read the datacube on the bench for the map seen above. See those two guards standing by the Black Gate entrance? Talk to them to learn that it's off limits and that you'll need to go to the SSC Office to inquire further. We'll do that after we get more than one reason to go there.
2: Head through the opening at the northwest section of the square. Take your first right, before the ladder in the distance (that leads to the small helipad). Enter Queequeg's Coffee. Talk to the manager behind the counter for a quest to investigate the lawsuit between Pequod's and Queequeg's at the SSC Office. Grab the office softkey at the top of the shelf behind two bags. Talk with David Kurczec to get the softkey to the curio shop above the Nine World's Tavern where you'll find the Omar. Nearby is NG Resonance, who you can talk to but nothing of consequence materializes from the conversation.
3: Take the offshoot hallway to his office, which you can unlock now with your softkey. Inside is a greasel, so prepare your best offense. After he's subdued, slip on in to grab the items on the table and in the safe, including a glass destabilizer weapon mod. Exit Queequeg's and keep right. Take the ladder up for a double-pack of multitools, and then head back down and continue to the Nine Worlds Tavern entrance. Talk with the two Order Seekers there to learn of the struggle between two factions, and enter the tavern.
4: Agree to the weapons lock, enter the stairwell and head upstairs. Use your softkey from David Kurczec to open the door and find the Omar. Before talking with the trader, head to the back right of the room, move two boxes behind a fallen bookcase, and you'll uncover the game's next secret weapon, the Assassin Pistol... a very nice weapon. It has a scope and increased range and damage. I decided to add a silencer and more damage as my modifications and used this weapon over the sniper as it takes two shots to the head to kill but uses less ammo. Talk to the Omar Trader and you'll have a chance to buy a BLACK MARKET BIOMOD CANISTER and more. If you do buy it, he'll tell you where you can pick it up, which I'll outline once we get to the ruins.
5: Head back downstairs all the way to the tavern. Open the first door you see on the right side and continue to a conference room with holocomm. View it to talk with Ava about a flight. It doesn't matter which option you pick. Another map is on a datacube on the table. Talk with Tracer Tong, a major player from Deus Ex, at the back of the room. He'll tell you of Her Holiness' kidnapping, give you a BIOMOD CANISTER and the code to the secret lab entrance in the Ruins.
6: Exit the room from the door opposite the one you entered, to find yourself in a long hallway. The door on the right leads to the bathroom with a multitool. The left locked one hides a nice stash of credits (400) and some items. Exit the hallway into the tavern using the other door in the hallway, and speak with Seeker Monica Platz for some story. Near the dance floor with NG jukebox you can listen in on the two fellas' conversation to learn of some weapon mods nearby. Sid Black is also here. You can hire him but I'd suggest sticking with Ava as Sid's a bit of a rip off, though Ava lacks his roguish charm.
7: Exit the tavern and take a right - it's just a big circle back to the square. Chad Dumier will contact you and ask that you meet him at the SSC. Further down the alley you'll encounter some Panzerwerk thugs bullying an Order member. You can approach them and pay 150 credits to leave him alone, watch them fight, or intervene. Continue following the path around back to the square and enter the SSC Office. In the main room, talk with Vera Maxwell, head through the door and then enter her office on the right for a few items.
8: Leave the office and enter the Evidence room at the back. Close the door behind you, equip a weapon with a glass destabilizer weapon mod, or add it to the weapon of your choice (I used it on my boltcaster as it was already silenced), and shoot the glass. Through the window and to the left is a camera. Disable it with your Spy Drone or EMP (or Mag Rail alt-fire), and enter the evidence room for a very nice collection of items, including a BLACK MARKET BIOMOD CANISTER. Read the datacube at the base of the right side of the lockers for the information Queequeg's manager wants. Seems both companies are one and the same. Leave the room and head into the nearby stairwell. Underneath are some items.
9: Take the stairwell up and enter the Observation room at the end of the hall. Watch Chad Dumier's interrogation of Saman, and then he tells you walk around to meet him. Enter the Visitation room, talk with him about Her Holiness, and receive the front gate code to the Black Gate Ruins. If you left Liela Nassif alive in Cairo, he also gives you a BIOMOD CANISTER. Exit the SSC building to the Trier Square and use your new keycode on the gate to enter the Black Gate Ruins.