Deus Ex 13th Mission: Area 51

The 13th and final mission in Deus Ex takes place in Area 51. In this mission, JC Denton must infiltrate the underground bunkers of Area 51 to go after Majestic 12 leader Bob Page.

Goals

 * * Given if you stray too far from Station 5 in Sector 2

Augmentation canisters

 * Bunker
 * Augmentation upgrade canister – In the basement of the comm building, locked inside a container (9378)
 * Sector 2
 * Augmentation upgrade canister – In the barracks, in the first chamber on the left (0169)
 * Regeneration / Energy Shield (appearance #2) – In the barracks, in the second chamber on the right
 * Sector 3
 * Augmentation upgrade canister – In station 17, which is accessed at the top level of the stairwell, locked inside a container (9378)
 * Sector 4
 * Augmentation upgrade canister – In the cloning bay, on the body of a dead scientist

Weapon modifications

 * Bunker
 * Accuracy – On top of the westernmost shipping crates to the SE of the starting position. To obtain the modification, jump on top of the inclined crate, then jump across the gap with the MJ12 trooper below, and travel along the right-side edge to reach the top of the westernmost crates.
 * Laser – Enter the Area 51 interior using the ventilation shaft accessible from the Hangar. When you drop down into the water, swim north to find the mod on a dead soldier.
 * Sector 4
 * Recoil – In the southwest portion of the middle level, inside a foot locker near a dead mechanic.

Bunker
Jock drops you off near the control tower. If you failed to discover the bomb on Jock's helicopter back at Morgan Everett's Home, Jock's helicopter will explode shortly after flying off.

Head to the comm building. If you did not kill or knock out Walton Simons in the previous mission, he will confront you here. Inside the comm building, the NanoKey to the control tower is found near a dead body. There is also a hatch to the basement, which is openable using your keyring. The basement includes an augmentation upgrade canister (9378), and a datacube for the login for the security terminal in the control tower.

There are two ways into the bunker:
 * Blast Doors – The blast doors can be opened by the security terminal at the top floor of the control tower (a51 / xx15yz). After entering through the blast doors, you may restore power to the elevator using a panel in the power station in the room to the right, and then take the elevator down to the entrance to Sector 2. Alternatively, you may jump down without using the elevator.
 * Ventilation Shaft – Inside the hangar, there is a large fan housing lit by blue light. The fan housing can be entered via a locked door near the floor or through its ceiling hatch. Once inside, destroy the fan and jump into the shaft, landing in the water below. Step out of the water and pass through a series of corridors and ladders to reach the entrance to Sector 2.

Sector 2
The initial area is guarded by a turret and a laser grid. After passing the laser grid, you will come across a generator that explodes. Near the generator is a holographic communicator. Use the communicator to speak to Morgan Everett. Everett will present to you one of the possible endgames, which is to kill Bob Page but preserve Area 51, and join the Illuminati in ruling the world as an invisible hand.

From this point, you may proceed directly to Sector 3 by traveling east and then south to reach a well-guarded room where the Sector 3 access door is found. Alternatively, you may use the code (8946) given to you by Everett to explore the recreation room and barracks accessible within the hallway. The recreation room contains a datacube with a code (0169) to the first bed chamber on the left side of the barracks. This chamber includes the NanoKey to the Sector 3 access door, as well as an augmentation upgrade canister.

When you're ready to enter Sector 3, open the access door, summon the elevator in the next room, and ride the elevator down to the entrance to Sector 3.

Sector 3
Before you enter the Sector 3 doors, Tracer Tong will present to you the second endgame option. Tong wishes that you destroy Area 51, to the effect of shutting down the Aquinas hub used for global communication. The result would be a new dark age, but one that is free from the tyranny of both Majestic 12 and the Illuminati. Tong also provides you with a map of Sector 3 (see the "maps" section of this article for the annotated version of this map).

The primary objective in Sector 3 is to speak with Helios at the Aquinas Hub. The Aquinas Hub can be accessed through the door in the stairwell marked "Aquinas Hub Access Door." To get the code to this door, first find a datacube in the coolant filtration area with the code (2001) for the door to the reactor lab. Then, enter enter the reactor lab and speak with the mechanic, who will give you the code (1038) for the Aquinas Hub access door. The room upstairs of the access door includes an augmentation upgrade canister locked in a container (9378).

Passing through the Aquinas Hub access door, find a ladder that leads downward. Then, go north, then east (traveling over the trench-like path labeled on the map as "Nexus 24"), and continue to the Aquinas control room. There, take the elevator to top level of the Aquinas Hub to speak with Helios. Helios will present to you the third endgame option, which is to merge with Helios so that you and Helios may govern the world together.

After speaking with Helios, the door to Sector 4 will be open. The door to Sector 4 is at the end of the "Nexus 24" path that you passed over to get to the Aquinas control room. To get to this corridor to Sector 4, you may head south from the room where friendly bots have been released, and drop to the corridor below. Alternatively, head back to the ladder to access the stairs leading downward to the path to Sector 4.

Sector 4
Sector 4 is the final map segment of the game. You may notice that there's an immediate change in compass direction during the map segment transition. North in the previous map segment now corresponds to East in this map segment.

The first area is the cloning bay. If you immediately turn left and travel forward, you may get hit by a flying door. The next area is the grays lab. If desired, the radiation in the grays lab can be shut down via the security terminal at the entrance (graytest / lab12). The terminal can also be used to open the exit door (alternatively, use the code 4167 on the keypad). You've now arrived at the nanotech infusion chamber, where Page is preparing to merge with Helios.

This final area is divided into three levels (top, middle, and bottom levels). The top and bottom levels are connected by a ladder and an elevator at the south of the map. The middle level is accessible by stairs from the SE corner of the bottom level. Each of the three levels has a Universal Constructor that will produce enemies endlessly until you've closed the lockdown doors in their respective rooms. The top, middle, and bottom UCs produce Mini-Spider Bots, grays, and Karkians, respectively. Note that Page's nanotech infusion chamber on the top level will drain your bioenergy when you get too close, but is otherwise harmless.

You must now choose one of the three possible endings, each requiring a different course of action:
 * Merge with Helios
 * To merge with Helios, you must enter the Aquinas router room to deactivate the two uplink locks. The router room is on the upper level, and can be accessed immediately after speaking with Page if you are able to bypass the keypad with a 90% bypass strength.
 * If you are do not have the multitools to bypass the keypad, you'll need to enter the Aquinas substation located on the bottom level. The Aquinas substation can be accessed through a door on the bottom level (6188), or through the elevator near the router room. Access the security terminal (Page / uberAlles) to open the door to the Aquinas router.
 * Once inside the Aquinas router room, deactivate the two uplink locks.
 * Then, return to Sector 3 (the previous map segment) and got to the top of the Aquinas hub where you spoke with Helios earlier. This completes the game for the Helios ending.
 * Join the Illuminati
 * For this ending, you'll need to shut down 4 blue-fusion reactions. All four reactors are located in the final area and are shut down by the code 7243:
 * One reactor is located on the upper level. Go to the south of the map, then head west, and then north, to arrive at the first reactor.
 * Two reactors are located on the middle level. One of them is directly under Page's chamber. The other is at the SE corner of the middle level.
 * One reactor is located on the bottom level, in the middle.
 * Once you have shut down all four reactors, return to the top level, and press the button at the Nanotech Infusion control station. This completes the game for the Illuminati ending.
 * New Dark Age
 * For this ending, you'll need to enter the coolant control room at the NE of the bottom level. You may enter through the main door (9248), or enter swim there from the central room on the bottom level. Inside the coolant control room, activate the button that cuts off coolant to the reactor.
 * Next, return to Sector 3 (the previous map segment). Go to the reactor control room. Activate the three ion injectors on the wall. Then, initiate the antimatter-matter reaction by pressing the button on the control panel. This completes the game for Tracer Tong's ending.