Deus Ex 5th Mission: Secret MJ12 Facility and UNATCO Headquarters

The fifth mission in Deus Ex takes place in the Secret MJ12 Facility on Liberty Island and the UNATCO Headquarters. In this mission, JC Denton must escape from his Majestic 12 captors. This is the last mission to feature the UNATCO Headquarters.

Goals

 * * Given by Paul Denton, if he and Anna Navarre are still alive.
 * ** Given by Alex if Anna Navarre is still alive.
 * *** Given if you reach the exit on level 1 before speaking with Alex.

Collectibles

 * Secret MJ12 Facility
 * Augmentation Canister: Aggressive Defense System / Spy Drone – In the nanotech lab
 * Weapon Modification (Accuracy) – Sold by a mechanic in Robot Maintenance
 * Weapon Modification (Range) – Second floor of the armory
 * Weapon Modification (Silencer) – Second floor of the armory
 * The Plasma Rifle is obtainable for the first time, found on the second floor of the armory
 * UNATCO Headquarters
 * Augmentation Canister: Regeneration / Energy Shield – Near Jaime Reyes
 * Augmentation Upgrade Canister – Sam Carter's armory
 * Weapon Modification (Recoil) – Sam Carter's armory
 * Weapon Modification (Range) – Sam Carter's armory

Detention
You begin in your cell without your equipment (unless you use an exploit; see "notes" section below). A mysterious figured called Daedalus then opens the cell door. Turning to your right, a MJ12 trooper is getting up from his desk. While he's turned away, use the baton to open the crate to obtain a riot prod. Use the riot prod or other weapon of your choice to take down the trooper when he returns to his desk.

The locked cells can be opened using the code 4679 provided by the datacube on the desk. One cell holds a medbot and a dead body with a PS20 and 2 lockpicks. The other cell holds the NSF soldier Miguel. You may invite him to join you in your escape. Miguel's death will not affect the progress of the mission, but if you intend to keep him alive, it is best to have him wait in his cell until you clear the path of all hostiles.

The file cabin to the right of the desk holds additional ammo and two multitool, one of which is in the locked compartment. If you wish to head straight to the armory to retrieve your equipment, these multitools can be used to open the door to the armory.

The room has a camera that will activate the turret, but it is possible to leave the room undetected by moving along the wall. When you are out of the detention area, Daedalus will provide you with a map of the facility. If you wish to retrieve your items, turn right to head toward the armory. There is also a floor vent that leads to the command center and the nanotech labs.

Armory and Robot Maintenance
The Armory, where your items are stored, is accessed through Robot Maintenance. If you happen to be detected while passing through Robot Maintenance, there is an empty space in the corridor leading to the armory where you can hide. The armory is guarded by two Delta-2 Peacebringer robots, but they are easily avoided due to their slow and predictable movement. The armory has doors on two sides, either of which can be opened by a multitool or by the code 2971, which is obtainable from a datacube in the offices on the top level of Robot Maintenance. Once inside the armory, there is a terminal in the upstairs room that allows you to disable the two patrolling bots. The upstairs room also has weapon modifications and a plasma rifle locked in a container (5239).

Nanotech and Medical Labs
While well guarded and not part of any mission goal, the nanotech lab is worth visiting because it includes an augmentation canister for the cranial slot. The nanotech lab is attended by P. Sherman, the man in black in charge of your planned interrogation. He will attack you on sight.

The back area of the nanotech lab has a grate near the floor. The grate leads to an area below, which is guarded by a Greasel. Entering the area provides a 100 SP exploration bonus. A file cabinet in the nanotech has locked compartments containing a datacube with all logins and passwords for the UNATCO headquarters, and another datacube with the code (0199) for the medical lab.

Before Daedalus gives you the code to escape from the MJ12 facility, you will need to visit the Medical Lab to retrieve data from Paul's datavault. Paul will be dead or alive depending on your actions in the previous mission. Once you have retrieved the data, Daedalus will give you the code (1125) for the exit near the command center. Once you leave the area attended by the guard, you will not be able to return to the MJ12 facility.

UNATCO Headquarters
Exiting the MJ12 facility, you find yourself in the familiar headquarters of UNATCO, except that all the guards will now be hostile. Straight ahead is Jaime's medical bay. Speak to Jaime. Your conversation with Jaime will affect his next destination. Be sure to pick up the augmentation canister that Jaime got for you. The canister provides a choice between Regeneration and Energy Shield. Both options have their respective benefits, but most players will likely find Regeneration to be more useful.
 * If you tell Jaime to go to Hong Kong, you will be able to meet him again in Hong Kong, where he will provide you with an augmentation upgrade canister.
 * If you tell Jaime to stay at UNATCO, you will be able to meet him again in Paris, where he will provide you with the killphrase for Gunther Hermann.

To escape the headquarters, you will need to meet with Alex Jacobson to obtain the NanoKey that unlocks the exit. JC suspects that Alex was posing as Daedalus, but Alex denies knowing anything about this supposed hacker. If Anna Navarre is still alive, Alex will not give you the key until you have killed her.

Other notable interactions in the headquarters: If Anna Navarre was not killed in the previous two encounters, she will intercept you on your way out. If you found the two parts of her killphrase (part of the killphrase is on Navarre's own computer in the makeshift office on the way to the level 3 jail, and the other part is on Manderley's computer), you will automatically tell Anna "Flatlander Woman" and she will self-destruct. Otherwise, you will have to fight.
 * If you speak to Sam Carter, he will finally let you into his armory, where you can find an augmentation upgrade canister.
 * If you run into Shannon, she will reveal that she was the one who was stealing from Sam's armory. She also offers to sell you scramble grenades.
 * Visit Joseph Manderley for a humorous interaction. Walton Simons, speaking through hologram device, will tell you that you'll be "dead in twenty-three hours. Another fifty billion dollars down the drain." If you kill Manderley before speaking with him, the dialogue with Simons will be somewhat different.

Once outside of the headquarters, head to Jock's helicopter to leave for Hong Kong. Jock will tell you that he was tipped to meet you by Daedalus. If Miguel followed you all the way to Jock's helicopter, he will part ways, telling you that he can make it on his own.