Deus Ex 12th Mission: Sub Base, Ocean Lab, and Missile Silo

The 12th Mission in Deus Ex takes place at Majestic 12's Sub Base and Ocean Lab, and later at a missile silo occupied by Majestic 12. In this mission, JC Denton must infiltrate the Ocean Lab to retrieve a schematic needed by X-51 to complete its Universal Constructor. In order to reach the Ocean Lab, JC must first steal a mini-submarine from the Sub Base.

Augmentation canisters

 * Ocean Lab - Universal Constructor facility
 * Augmentation upgrade canister – On the body of a Man in Black in the electrified water at the east side of the facility
 * Sub Base
 * Augmentation upgrade canister – After returning from the Ocean Lab, Gary Savage will give you an upgrade canister if you saved Tiffany in the previous mission

Weapon modifications

 * Sub Base
 * Silencer – In the command module, on an a round table where a scientist is sitting
 * Ocean Lab
 * Clip – In the south wing, accessible by swimming into a hole with a flickering light south of the URV bay
 * Recoil – In the observation section, accessible from the excavation area
 * Reload – In the left locker in the SW room of Crew Module Deck One (the upper deck)
 * Laser – In the left locker in the SW room of Crew Module Deck One (the lower deck)
 * Missile Silo
 * Range – In the guardhouse at the SW corner of the map, inside the right-side footlocker
 * Silencer – Inside the locked semi-trailer, at the very back behind the large metal crates

Sub Base
The Sub Base is a series of interconnected platforms referred to as "modules." The command module (labeled as the "main building" in Tiffany Savage's hand drawing) is located onshore, whereas module 1, module 2, and the URV bay are located in or above the water. There are two ways to enter the sub base: Inside the command module, you can encounter a scientist named Dr. Pinkerton, who will give you a map of the Ocean Lab. Also in the command module is the Karkian tank (code 1223). Stepping into the tank yields a 50 SP bonus. Another 50 SP bonus can be obtained by entering the closet of the room to the north, where there is a scientist is sitting on a round table. A silencer modification is found on this table.
 * Main entrance – The main entrance to the command module is at the bottom of the largest on-shore pillar. The key to the main entrance is in the nearby supply shed. Entering the supply shed will result in a bonus of 149 SP.
 * Swim route – As shown in Tiffany's drawing, module 1 has a ladder that permits access from the water. This alternate route gets you closer to the URV bay, but skips the SP bonuses associated with the command module.

Make your way to module 2 and take the elevator to the underwater section. Here, access a security terminal (Tech/Sharkman) to open the URV pool doors. Then, head to the URV bay and interact with a mini-sub to travel to the Ocean Lab.

Ocean Lab
You begin in the Ocean Lab's URV bay, which is level A1 on the map you received from Pinkerton. Your eventual destination is the building with the green beacons visible from the window (Crew Modules C1/C2 on the map). Despite the deep ocean setting, the Crew Modules cannot be reached by swimming, and can only be reached by travelling through the interior structure of the Ocean Lab.

However, if you wish to explore the ocean, there is a secret area in the south wing that will reward a 200 SP bonus. To reach this area, hack the terminal and open the doors of the URV bay. Swim out into the ocean, then turn right (south) to find an access hatch marked by red lights. You may enter the hatch to refresh your oxygen. Then, swim further south and find an open hole with a flickering light. Swimming into this area and then towards the office desk inside will yield the 200 SP bonus.

Continuing with the mission objective, from the starting position (the URV bay), head upstairs to the command center (level A4 on the map). From the command center, enter the room to the north. Here, on the left side of the hallway is a turret and a dead MJ12 Trooper. Pick up the NanoKey near the body and use it to open the door to the Greasel Lab on the north end of the hallway. Continue through the Greasel Lab and drop down the ladder to enter a partially submerged room. Here, there is a door that is locked by a keypad. The code to the keypad can be found on a datacube on the floor of the submerged area to the south (accessible through the unlocked door). Once you've obtained the code (5690), return to the area right below the Greasel lab use it to unlock the door to the Tunnel Checkpoint (the checkpoint is item T1 on the map).

From the Tunnel Checkpoint, proceed through the excavation area and enter the Crew Modules. On the lower deck of the Crew Modules, find the Deep Lift that takes you to the bottom level of the Ocean Lab. From there, proceed forward to reach the Universal Constructor facility.

Ocean Lab - Universal Constructor facility
Continue to the east end of the facility, where you'll find a pool of water. Note that an augmentation upgrade canister can be found on the body of the Man in Black in the water. Summon the elevator and ride it up. On the upper level, use the security terminal (MJ12/Skywalker) to activate the bridge. Cross the bridge, and use the computer there (MJ12/Skywalker) to upload the schematics to Gary Savage.

Return to the surface
You will need to return to the Sub Base to meet Gary Savage on the roof of the command module. On your way out of the UC facility, Bob Page will tell you through the holographic communicator that Helios intercepted your transmission and was able to access the data that Page needs to continue manufacturing the virus. Page will also suggest that Vandenberg is about to be attacked and reduced to rubble.

Walton Simons will confront you at the excavation site. Simons has 600 HP, a Plasma Rifle, and the Cloak augmentation. He is also immune to the baton, riot prod, and flamethrower, and will only take 10% damage from tranquilizer darts. If you attempt melee combat, Simons will pull out a Dragon's Tooth Sword. If you do not kill Simons here, he will later appear at Area 51. Note that the game does not make a distinction between dead and unconscious; thus, rendering Simons unconscious will have the same effect on the story as killing him (i.e., he will not appear at Area 51).

Once you've reached the roof of the Sub Base command module, Dr. Savage will inform you that MJ12 troops have occupied a missile silo to the north, and are preparing to launch a nuclear missile at Vandenberg Air Force Base. Your next objective is to stop the missile launch. If you rescued Tiffany in the last mission, Dr. Savage will give you an augmentation upgrade canister.

Missile Silo
From the starting position, you will need to infiltrate the walled base. You may open the locked front gate or infiltrate the guardhouse at the SW corner of the map and use the elevated catwalk.

Once inside the walled area, there are two routes into the underground facility: Inside the underground facility, use the code 8456 to open the first underground door. Use it again to open another door. Then, turn left and use it on the door labeled "launch command" (note that the other door, labeled "missile silo," is not accessible at this time). The next area is well guarded by Men in Black and MJ12 commandos. Head upstairs and press the abort button. Then, use the terminal on the left (Elder/Armageddon) to initiate a new launch, aimed at Area 51.
 * In the fenced area to the NE, there is a locked door (80% lock strength) leading underground.
 * The alternate route is through the vent inside the building with the repair bot. The door to this building is blocked. However, you may enter through the building immediately to the south.

The next goal is to check the missile launch site to make sure that MJ12 has not sabotaged the launch. The previously inaccessible door to the missile silo will now be open. Proceed through this door, and continue either through the long, narrow corridor guarded by Men in Black and commandos, or alternatively down a floor vent to the bottom of the silo. In either case, you will need to use the elevator inside the silo. The elevator has access to 6 levels. Note that level 4 has a repair bot.

Take the elevator to level 2, where you'll encounter MJ12 agent Howard Strong. Once he is killed, take the elevator to level 6 and exit the silo through the ladder. At the top of the ladder, activate the button to open the surface hatch. When you're done with the area, fly out on Jock's helicopter to complete the mission.