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From the subway station in Paris, you suddenly find yourself next to a large man having a conversation in Morgan Everett's home. Atanwe tells you that you can find Everett in his downstairs lab.
Don't bother taking the ramp near you down as it's a dead end. The other door in the room is locked and leads to the helipad which we'll use later. Instead head into the wide hallway leading to the next large room and take a left through the first door. Through the bedroom is a bathroom containing an aquarium nanokey and large mirror. Breaking the mirror will reveal a locked door. This is a purely optional part of this level and is related to another locked door later which can be bypassed with multitools on its keypad. Either room will have the key or code for the other room, so it's up to you whether you want to spend multitools or lockpicks.
Inside the locked room is an exploration bonus and datacube with the code 8001. Behind the wall you'll find Lucius held in cold storage yet alive and with the ability to talk. He was the former leader of the Illuminati and asks that you tell Everett he's cold, for a secondary quest.
Exit from the bedroom into the kitchen area, go through the door and down the stairs to a repair bot, then up another half set of stairs past a large double-sided aquarium, and take a left at the first junction. In the next room is Alex Jacobson. If you hack his computer, you'll get the codes 2384 and 6426, useful for containers shortly.
In the room after Alex's you'll find a large door with keypad and medbot. If you already unlocked and explored the room upstairs in the bathroom (at #2), you'll know the code 8001. If not, you can use multitools to enter this room and then get the nanokey inside for the locked mirror door. Inside is an AI entity called Morpheus. Talk to it multiple times to learn a little about yourself, and its purpose. Now head back out of Alex J's office and take a left into the corridor you were previously in.
Around the corner is Morgan Everett's lab. Talk to him multiple times to learn about his organization, and, if you saw Lucius upstairs, learn that he's not about to unfreeze him, though he has the technology to do so. Afterward, use the codes 2384 on the EMP Shield/Ballistic and Vision/Targetting AUGMENTATION CANISTER
S containment keypad. Use the code 6426 on the augmentation upgrade canister.
At the aquarium hatch, you can use the nanokey you got from the bathroom upstairs, dive in for a small bonus, and find darts and rebreather in the next tank.
Head back upstairs to the bathroom (if you've decided to take on this side quest), and into the locked door behind the mirror. Talk to Lucius for the first time or the second (see #2 if the first). You can choose to tell him Everett won't heal him, or even use the security computer terminal nearby to shut down his bio systems... perhaps euthanasia?
Time for our departure. Make your way back to the locked door in the room you began in. Use Morgan Everett's helipad key you now possess on the door and ascend the stairs to the helipad. Before taking off, notice the dead body on the ground. Now talk to the mechanic. You thinking what I'm thinking? Return to Everett and tell him about the strange mechanic and he'll tell you he's not one of his men, and order you to eliminate him.
Head back to the mechanic and talk to him. After the conversation, he bolts and turns enemy. Take him down whichever method you prefer, and talk to Jock, who would have died later if you wouldn't have discovered the imposter. After Jock makes the necessary checks to his chopper, he finds a problem and fixes it before you leave for Vandenburg... safely.