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1: Back in Cairo, you'll be dropped off where you were the first time, if you flew with Ava, at the Helipad just above Queequeg's Coffee in the middle of town. Head down the ladder and talk with Queequeg's Manager. Tell him the truth (if you found out the truth in the Trier SSC office awhile back) and he'll give you the keycode to Pequod's safe in Arcology. Sid Black is also here, and you can hire him now, but I'd still choose Ava for free.
2: Now turn left (if you're facing the Coffeehouse) toward the Medina Apartments, and talk with the Illuminati Elite Guard. To avoid a confrontation now, choose the "I understand" line. Continue toward the apartments and enter North Medina. Head up the first set of stairs and speak with the Omar Trader on the balcony for a BLACK MARKET BIOMOD CANISTER (which will cost you) and other items.
3: Back downstairs, take a right and head to the Order Mosque to talk with Leo, two-thirds the way to becoming an Omar himself. If you choose the "badass" line, you can follow him and watch him safely take down the Omar himself, and then you'll talk about meeting in New York. Walk past the Order Mosque to the news holocomm. If you've been listening to them, the T-A-L-K Bullet's have been kind of funny but annoying as well. Listen to this final one with Saman, and have a chuckle. Continue down this path to the back area and you'll find Lin-May Chen, who has some info on the Illuminati going to assassinate Paul.
4: Option time. You can continue into the apartments for a reward quest from Maskini Nassif on the 3rd floor, to wipe out some Templars on the 4th (one of which is Silas Archer), or you can skip them, it makes no difference to your objectives. When you're ready, head into the Order Mosque and hold up before you enter the first door. There are lots of Templars all around, including one PAP (Power Armored Paladin) just inside.
5: Open the door, and send your Spy Drone to the left or right to deal with two Templars and one PAP. Or, use your favorite method. Take a left at the T-intersection and then open the big doors to your right, that lead to the main chamber of the mosque. A huge military bot is inside, and you'll want to destroy it. Again, use your Spy Drone to take it down safely, or use the colums as cover while you take it down in other ways. When it's disabled, do not go in (or exit again from the same door) and continue downstairs toward the Infirmary. Three Templars are in the hallway beyond, but are far enough away that they can be shot or taken down from afar.
6: In the middle of this area, there's a medbot if you need it. Head into the Infirmary and talk with Mrs. Ameer, who will reward you with the keycode to a locker in the Arcology SSC Guard Station. If you talk with the Head Physician with your inventory full, he'll give you an "infinite" amount of medkits (- an obvious bug). Back upstairs, peek through the door to the main chamber where the mil bot was, and you can see a patrolling Templar on the other side. You can stay her to pick her off if you wish, and then head across and to the back of the Mosque. Another Templar is to the right. Upstairs, you'll find a couple harmless scientists and a chance to refill some of your ammo.
7: Take the Arcology Elevator at the back of the Mosque to Arcology 107-108. When you arrive, prepare for battle. There are several Templars in the area, one patrolling the ramp down to 107 and a PAP at the top of the ramp up to 108. A total of three normal Templars should join the fight when you engage the one on the ramp down (two from downstairs). There's a PAP downstairs, as well as another normal Templar and ceiling mounted gun turret near Pequod's Coffee. Use your disgression in taking on the Templars. Again, Spy Drone is the easiest way, but there are other easy ways involving wepons. When it's over, head downstairs to Pequod's.
8: Open the safe and collect your reward for telling the Queequeg's manager the truth, including an Increased Range Weapon Mod. Talk with NG in the corner and you'll get a quest to see if she is trapped on Arcology 110. Across the building at the SSC desk are a couple more normal Templars. Take them down from afar, and you can find another roaming the Tarsus Academy entrance.
9: Take the maintenance ramp down to Nanoformer Programming, nearby the SSC desk. By crawling through the cubby hold at the end of the ramp corridor, you can uncover the game's sixth and final secret weapon, the Widowmaker SMG near the body of a dead guard. Crawl back out and head left up to Nanoformer Programming. You'll notice a non-hostile WTO guard at the top, who tells you there's a prisoner inside. It's Klara Sparks.
10: Back up and take down the WTO guard, and the other two who come through the door once you engage the first. One of them is Donna Morgan. Inside, you'll find Klara Sparks, who rewards you with an Increased Range Weapon Mod. Climb the ladder down and you'll find a nice stash of items below including a BIOMOD CANISTER. Time to head to level 108 via the ramp up to 107, and then the ramp across from Pequod's. Beware the PAP at the top if you haven't dealt with him yet. Take a right and head all the way back to the SSC Guard Station door.
11: Inside the SSC Guard Station are three normal Templars and a ceiling turret. You can use Mrs. Ameer's keycode you received from the Mosque Infirmary to open the locker containing a couple weapon mods and other items. In the back room is an Increased Damage Weapon Mod. Exit the room and proceed to Arcology Air to its left, this level's climax.
12: When you step off the elevator, you'll talk to the Illuminati Elite Guard you saw down in Medina. Head down the ramp to your right and you'll receive another message from Saman. Right now, it doesn't matter which choice you pick, but choose the top one to annoy him. He'll let you know that you're safe for now from the Paladins. The Illuminati guard stops at the bottom of the ramp near the next room, and inside are two PAP's and one normal Templar, friendly enough for now.
13: Before you take any action, and while there are no hostilities toward you, head to Hangar 23, talk to Leila Nassif and receive a BIOMOD CANISTER, and use the repairbot if you need to. Enter the storage room at back to find NG in the flesh. You can go back and report that to the NG Hologram if you want but you'll get nothing as a reward. Head down the hallway behind the desk toward Hangar Bay 24.
14: Open the doors. For now, they'll be friendly until you talk with Dr. Todd ahead. Before you enter, I'll brief you. You'll be asked by Dr. Todd to give a sample. Your choice will be basically yes or no. If you choose no, you'll have to fight a few PAP's, a Military Bot and the Turret above. No one said rescuing him was going to be easy. However, it's not bad at all if you hide behind the crates from the Mil Bot (which isn't hard as he's lumberingly slow), Cloak/Thermal Mask and Spy Drone the Military Bot, and Biotox the PAP's. If your Biotox doesn't work on the PAP's, Drone them or use the Mag Rail, as it seems to work well. Just keep an eye on your energy. When it's over, take out the turret to the right of the control room above with your alt-fire from the Mag Rail, or other preferred method. Head up the ladder and recover Paul's belongings in a chest in the room.
15: Back below, activate the panel on Paul's cell and choose whatever option best fits your character (terminate or revive). If you revive him, you can still see every ending to the game, and it makes the end part a little easier in my opinion for doing so. This walkthrough will release him. If you gave your blood to Dr. Todd, none of this will of course have happened, and Paul will have already died. If you release Paul, you're going to face a couple more Illuminati at the control room above Hangar 23. However, if you decide to terminate Paul, you'll be congratulated by Chad Dumier and will face no more obstacles for now. JC is not pleased if that happens.
16: Leave the room, take the first left, climb through the vent behind the boxes, and up the ladder. Cloak if you revived Paul, as there will be Illuminati Elite Guards (IEG's) up here. Take a right at the top of the ladder, then a left and activate the Pilot Beacon to head to Liberty Island.
