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You've been captured and taken to their secret base, all your belongings stripped. Now what? A mysterious transmission from an entity called Daedalus tells you that your cell (in the area marked "Begin" on your map) is now unlocked. There's a guard in the next room, and in the crate before his desk is a prod with a baton on top. Use whichever you like to take him down. It's about this time that I generally don't care any more how I take out the guards. However, when I can spare them and they're not really actively attacking me, I'll prod or tranq them still. The rest I either avoid or, especially later in this mission and from now on, have less qualms about using my (by now) awesome sniper rifle and skills.
Read the datacube on his desk to get the codes for the detention block cells (4689) and door (4089). An NSF prisoner is in the northwest cell. Use code 4689 on the keypad and have a chat with him. I'd tell him to stay where he is when the choice appears. Time to exit the detention area.
There's a security camera on the right side of the room next to the hall leading out. Slip underneath and use code 4089 on the north door (if it's not open). If the camera spots you it's okay, just creep out into the hall until it quiets. There are no immediate guards out here. You'll see a floor grate at the junction of this hallway and another. We'll be going down it after you get your equipment from the armory to the south.
Head to the right and down the stairs to #1, which is a 3-story robot maintenance area, and you'll be on the lower level. There's a guard here in the area, so sneak up and take him out, but be careful of the guards patrolling the open walkway above, who will fire on you if they spot you. Take the northeast stairway up. The #2 hallway is where we want to be, and you'll need to watch out for the guards patrolling the area. There's a handy niche you can hide in before the indicated hallway with a couple stacked crates. There's also an orange uniformed worker walking around who will talk to you and sell you the security access codes for the area, but if you can hack, it's not worth it.
Proceed up the stairs to #3. The guards walking below can still see you through the window so be careful. There's a switch in the central area of this upper level that lowers the security bots down to the lower level. You can change their behavior using the computer panel on the wall nearby. In the room at the end is a guard sitting at his desk. You can sneak up and prod him for an easy takedown. Now read the datacube on his desk, which gives you the code to the armory, 2971. Exit back to the lower level, use the repair bot if you need it, and proceed south up the stairs to the armory area at #4, but beware giant robot(s) slowly walking circles around the armory.
Wait in the niche along the right wall before the armory for the robot(s) to pass, and head straight south to the door. Use the access code 2971 on the keypad, and beware a guard inside. Take him down, and then head upstairs to use the security computer terminal to deactivate the robots circling the armory, and the camera downstairs as well. Now have a field day picking up your equipment and new equipment downstairs and up. Hack the computer downstairs to learn the code for the container upstairs with the plasma gun, 5239.
When you're through in the armory, head all the way back (not really that far) to the floor grate we saw earlier, just north of the detention block at #5. Open it, descend, and head right. We're going to to the nanotech lab. Follow the tunnel north, ignore the coming branch to the right (which we'll take when we come back here next time), and continue on. Follow it until you come to an intersection with grates on both sides. Take a left to the immediate dead end and head up the small ladder to the grate.
Beware of a guard walking above and wait for him to be out of view. When it's clear, climb through the grate and head a few large steps north to the hallway at #6 (with stacked crates). There will be a doctor standing just inside who will initiate conversation. It's Dr. Moreau, who will give you the code to the medical area, 0199.
Head east (right) to the medical area and you'll pass a room on the left with a guard and secretary talking. Carefully sneak past this and up the stairway on the right side near #7.
You come to a room with a datacube containing the computer login MJ12 and password "invader". There's a locked grate on the wall. Pick it and follow it to the ladder at the end. Descend it and you'll find the medical lab at #8 with Paul awaiting you.
Have a chat with Paul, and then read the two datacubes in the room. Daedalus gives you the code for the exit door, 1125. Walk near the exit doors with the guards to receive a rather large 500 point skill bonus. Now climb the ladder and backtrack all the way back to the grate near the #6 hallway that you emerged from, in the nanotech lab. We're going to take that other branch we skipped last time to get to the office in the nanotech lab at #9. Simply follow the vents back toward #5 the same way you came in, only take the first left (which was a right on your way here). There's a dead animal carcass ahead to mark your path.
At its end is the office we're looking for at #9. Inside is a Man in Black (MIB). The best way to take him out is with a prod or tranq so he doesn't explode away his belongings. Sneak up and do that when he's not looking. You might alert the guards in the next room somehow, so if they come, take care of them as well.
Take the MIB's nanokey and you'll have access to the locked file cabinet drawers. Use the nanokey ring on all the file drawers you can, and read the datacubes for more login codes. Unlock the top right drawer for the login "psherman" and pass "raven". Use that on the computer in the room to open the AUGMENTATION CANISTER
container field. There's a medbot in the next room if you clear it of guards who can heal and install the Aggressive Defense/Spy Drone aug you just retrieved. I'd recommend the Spy Drone, as there are several spiders and bots later that can be disabled with the drone's EMP blast.
Re-enter the grate and head back to the #5 entrance to the vent systems. Now take the other direction, west, toward #10, the Command Center. We're almost out. When you emerge, defeat the guard in the room and be careful of the dog and MJ12 patrols around the perimeter of the room. Stand against the west wall and eye the exit door to the west. When the coast is clear make a run for it and use the code you got from Daedalus, 1125. Proceed through the corridors to where the map says "End," and guess where you end up? Yup, UNATCO HQ!
Sam Carter, Jaime Reyes and Alex are your allies here. Find them all in their office. If you decided not to kill Anna back in the 747, then you're going to have to kill her here eventually. This time, Sam lets you into his Armory which is nice. Alex will give you the key to escape (and if you haven't yet taken Anna down, includes killing her in the bargain). Finally, you'll have a choice with Jaime. Either have him stay here as a spy or have him meet with you in Hong Kong. If you keep him here, he'll meet up with you in Paris about Gunther's kill phrase. And if you meet him in Hong Kong, he'll give you an Augmentation Upgrade. When you're finished with these three and the medbots, and the exploration, see Manderley on level 2.
Walton Simons will be a holo in his projector and alert him to your presence. After the conversation, and as you leave, Manderley will attack you so be prepared. If you need to kill Anna, hack or break into both Manderley's and Anna's computer for her two kill phrases. You can use the code Paul gave you, "demiurge" and "archon" or their own codes you have previously. Head back to Alex for the exit key once you kill Anna. If you already have it, head out... and watch for guards on the way. You're about to go to Hong Kong, so see the chopper and Jock outside to end the mission.