Deus Ex Walkthrough – Secret MJ12 Facility

• Introduction
• Liberty Island
• Battery Park
• Hell’s Kitchen
• Warehouse District
• Mole Tunnels
• Airbase
• 20th Street Warehouse
• Secret MJ12 Facility
• MJ12 Helibase
• Tonnochi Road
• VersaLife
• Hell’s Kitchen 2
• Naval Shipyards
• Cemetary
• Paris Catacombs
• Champs Elysses
• Chateau DuClare
• Cathedral
• Vandenberg
• Gas Station
• Sub Base
• Missile Silo
• Area 51
• Conclusion
• Saves

Secret MJ12 Facility

Having been captured it is no surprise that all of your weapons have been taken from you (you are left with just your nanokey). However, somehow you have managed to hold onto all your ammo and cash! Exit your cell as soon as the power is cut and take the baton from the crate to the right. The guard will now walk around the corner. Hide yourself behind the filing cabinet and take the combat knife that is lying on the top. Kill the MJ12 trooper as he walks back past you. He will provide you with a pistol. 3 of the drawers in the filing cabinet are unlocked. Inside 2 of them you will find 1 mulitool, 1 forty and 1 pack of cigarettes. There is a riot prod in the crate, a datacube on the table, and you can take the fire extinguisher at the other end of the corridor by breaking the glass. The datacube will have provided you with a code to open the doors to the other cells. In one of the cells is a medical bot and a dead body which is carrying a PS20 and 2 lockpicks. Another cell has 2 soy foods inside. The last cell has another prisoner (Miguel). Speak to him and he will tell you that he thinks Paul is dead and he will give you 1 medkit. Tell him to wait where he is for the moment. Avoiding the camera, leave the detention area. This should get you 250 skill points. In front of you and slightly to the right is a vertical pipe in the wall. Behind it you will find 1 lockpick and 1 crowbar.

Go through the hatch in the floor and head Northwest. You will come out in the command centre. Kill the MJ12 trooper who is patrolling in this room and take his assault shotgun. You will find 1 pack of cigarettes, 1 gas grenade, 1 fire extinguisher and 1 assault rifle on the tables in here. Use the security computer terminal to switch off all the cameras and set the turret to enemies. Around the outside of this room there are 3 MJ12 troopers and 2 dobermans. Take care of them now. Go through the passage marked ’laboratories’ and speak to the doctor you meet there - he gives you the code to the medical area. Take the gas grenade from the crate on the top of the pile of boxes in the corridor. Enter the nanotech laboratory and immediately go down one of the hatches in the floor. Towards the South there is a turning to the East which you should take. Then take the next turning to the left and continue to the end of the tunnel. Open the hatch and follow the man in black as he walks to his chair. Open the hatch in the wall as you go past it. Now, whilst standing behind the seated man in black, hit him with the baton and quickly hide through the hatch that you just opened. You will inevitably lose some health here, but there is a medical bot nearby. Continue along the tunnel you have entered and go down the ladder that you find. You will get 100 skill points. Kill the greasel that is in the water and take the 12 plasma rounds and ballistic armour from the crates. Go back up the ladder and out into the laboratory (after the alarm has stopped and the man in black has returned to his seat). Now hit the man in black with the baton again and hide until he sits back down. Keep doing this until he is rendered unconscious (this prevents him from exploding).

All men in black and women in black as well as certain augmented people such as agents Navarre and Hermann and Walton Simons and also all bots will explode as they are killed to erase all evidence of themselves. If they are carrying any useful items then these will be destroyed in the explosion as well. To get round this you must use non-lethal methods such as the baton to take these enemies down if you want to take an item that they have. Then you can kill them by destroying the body afterwards.

From the man in black you can get a stealth pistol and a nanokey. Now you can kill him. Take the 4 tranquilizer darts from the table and look at the 2 datacubes and take the medkit from the crate in this room. You can use your nanokey to open all but one of the drawers in the filing cabinet in this room. Take the multiool from inside and look at the datacube. Using a combination of the cage release button by the door to this area, the button to close the door and your own combat knife, it is possible to kill the 2 MJ12 troopers and the 4 greasels in the adjoining room without any of the doctors or scientists being killed. One of the MJ12 troopers is carrying a mini-crossbow that you will want to pick up (also giving you 2 +/- 2 tranquilizer darts) so make sure the greasels don’t consume his body before you take it! Go back into the previous room and access the personal computer terminal. Use it to open the containment field, allowing you to take the augmentation canister that is inside. Use the medical bot in the next room to install the spy drone augmentation as well as to get your health back up to 100%. Get out into the corridor and head back to the command centre. From here take the passage that leads past the detention area. Keep going and you will come out in the robot maintenance section.

Go to the right and you will find a scramble grenade and a bioelectric cell in a crate. Kill the MJ12 trooper who is on the lower level and then make your way up the stairs on the left. Take out the MJ12 trooper patrolling this level (the sniper) and take his sniper rifle and 3 +/- 3 rounds of 30.06 ammo (you will have to drop 2 packs of cigarettes and 2 fire extinguishers to make room in your inventory). Go through the passage leading off the Northwest corner of this level and kill the MJ12 trooper patrolling this route. There is 1 lockpick behind the vertical pipe in the wall along here. Proceed up the stairs and kill the MJ12 trooper who is behind the desk. Check the datacube on his desk and then go through to the office accross to the right and kill the MJ12 trooper there. Here you will find another datacube and 1 lockpick. Drop your forty in order to pick up the 2 EMP grenades on the other table here. Use the security computer terminal to alter the AI of the bot on the ground floor, resulting in it being on your side. Get back down to the walkway around the main room below and find 1 multitool on a box by the 2 inactive bots to the South. Go down to the ground floor and find another 2 multitools: one in each of the bays to the South and Southwest, on boxes.

Continue along the passage to the South. There are 2 heavily armed military bots here, but so long as they aren’t facing you, they won’t even know you exist. While they aren’t looking, run up to the nearest door to the armoury and use the code from the datacube earlier to open it. Here you will get 150 skill points. Kill the MJ12 trooper inside, but beware of the camera and turret. Go upstairs to find the security computer terminal with which to switch off the camera and set the turret to enemies. Also choose to deactivate both the armoury bots. Now it is time to recover your weapons so get downstairs again. Firstly drop the following: 1 stealth pistol, 1 assault rifle, 1 assault shotgun, 1 ballistic armour, 1 scramble grenade, 2 soy foods, 1 PS20, 1 crowbar, 1 riot prod and 1 baton. Pick up 1 gas grenade, 1 EMP grenade, 1 LAM all from the shelf. Also collect the mini-crossbow, sniper rifle, GEP gun, flamethrower and pistol from the same shelf. You will get 4 tranquilizer darts and 6 rounds of 30.06 ammo from these. Also you should notice that these weapons still have all the weapon modifications that you applied to them earlier. Phew, you hadn’t collected all the modifications in vain! Take the sniper rifle from the desk to get another 6 rounds of 30.06 ammo and find the 1 LAM in one of the crates. If you try to pick up the items from the other shelf you will be told you can’t carry any more of them. To get round this you must first drop the 1 bioelectric cell, 5 lockpicks, 2 medkits and 5 multitools. Then you will be able to pick up the ones from the shelf, giving you 30 bioelectric cells, 20 lockpicks, 15 medkits and 20 multitools. Go upstairs and take the 6 rounds of 30.06 ammo and the mini-crossbow to provide you with 4 tranquilizer darts and the 4 darts and 4 flare darts. You have managed to recover all the items from your inventory prior to the capture except for the rest of your grenades! There are also two weapon modifications here. Apply the silencer modification to your sniper rifle and the range modification to your pistol.

Return to the previous area where there were 2 repair bots. Speak to the mechanics. One of them will offer you some items. Buy the accuracy weapon modification for 750 credits and apply it to your sniper rifle. Pick up one of the nearby TNT crates and head back towards the laboratories area. Keep going, following the sign on the wall that says medical R and D. Crawl past the office making sure that the trooper and secretary don’t see you (if they do they will set off the alarm and you will have to deal with many more enemies at once). Go up the stairs to the right and you will find a datacube on a table there. Now go back down the same stairs and crawl straight past the door to the office, then go up the other stairs which you find. Gently put down the TNT crate and kill the MJ12 trooper. Use the security computer terminal to switch off the camera, set the turret to enemies and open the door. The karkians will leave their chamber and kill the 2 MJ12 troopers guarding the medical room. Take the TNT crate down the stairs and watch as this happens. Throw the TNT crate at the 2 karkians to kill them. Make sure you do this before either the nurse or doctor run out of the medical area or they will be killed too. Go through the door to the medical area (you have the code if it is still locked) and you will get 500 skill points. Walk up to Paul’s body and you will get another 500 skill points after Daedalus sends you another infolink message. It is this second set of 500 skill points that you would not have got if you had saved Paul earlier. If anyone has managed to get this whilst still saving Paul, please let me know how! Like I said, I am unsure whether this is supposed to happen or if it is a bug of some sort, but as it stands you get more skill points this way by letting Paul die. There are 2 datacubes in this room. Now go back to deal with the MJ12 trooper and the secretary in the office. In order to totally complete this section you should now go back to the robot maintenance area and use your combat knife to destroy the 2 military bots and the 4 security bots (not the friendly one) on the upper level (you will have to use a medical bot in between to regain health). Pick up the second TNT crate from the lower level of this area and return to the detention area and tell Miguel to stay close. Lead him to the far side of the command centre and open the door using the code that Daedalus gave you. Put down the TNT crate and tell Miguel to wait here while you go round the corner and kill the MJ12 trooper sitting behind the desk. He has 2 +/- 2 tranquilizer darts on him. Pick up the TNT crate and tell Miguel to stay close again. Continue along the corridor and make sure Miguel is still with you after the map change.

NYC - UNATCO HQ

Being careful of the UNATCO trooper ahead, lead Miguel through the door in front of you. You will get 200 skill points here. Put down the TNT and tell Miguel to wait here and then kill the UNATCO trooper. Lead Miguel up to the medical area and tell him to stay there. Speak to Jaime Reyes and ask him to meet you in Hong Kong. Take the augmentation canister that he gives you and use the medical bot to install the regeneration augmentation.

You should realise that the regeneration augmentation effectively lets repair bots function as medical bots as well. If you are damaged, simply activate the regeneration and you bioelectric energy will be used to improve your health. Then go up to a repair bot and replenish your energy.

Speak to Alex Jacobson in computer ops and he will give you a nanokey. Check his secret area where you will find 600 credits. There are 4 UNATCO troopers to be killed on level 3: one in the men’s restroom, 1 near Anna Navarre’s old office and 2 more by the cells through her office. One of them is carrying 2 +/- 2 tranquilizer darts. See Sam Carter and he will let you inside the armoury this time. Apply both the range and recoil weapon modifications to your sniper rifle. Use the augmentation upgrade to improve the newly installed regeneration augmentation. Go up to level 2 and find Manderley speaking to Walton Simons in his office. Manderley will draw his gun on you so make sure you kill him before he kills you! Leave Janice Reed alone as she doesn’t seem to be considered an enemy. Kill the 2 UNATCO troopers in the conference room as well as the UNATCO trooper in the break room who is currently watching TV. Speak to Shannon by the ATM, but don’t buy any scramble grenades. Don’t bother hacking the ATM - you can’t withdraw any credits from it this time. Up on level 1, one of the offices has a datacube and the other has 1 UNATCO trooper to be killed. Go through the exit door on level 1 (use your nanokey) and get the attention of the UNATCO trooper guarding the retinal scanner. Kill him as he leaves his post to get you. You might notice that this trooper is called Scott, however if were paying attention earlier you will have found that the first UNATCO trooper you killed after your escape was also called Scott. Were there 2 Scotts that you knew in UNATCO or did he come back to life after you killed him the first time? Anyway, go back to collect the TNT crate and get Miguel to follow you to level 2. Tell him to wait in the corridor while you use the TNT crate to open the locked cabinet in the conference room. Take the 12 plasma rounds and 12 Sabot rounds that are inside. Lead Miguel through the retinal scanner door above level 1 and head for the exit to the HQ. This gets you 165 skill points.

NYC - Liberty Island

Kill the last remaining UNATCO trooper (private Lloyd) and exit the building. Find the EMP grenade that is in a crate through the hatch in the ground by the communications van (use your nanokey to open it). Lead Miguel to Jock’s helicopter and speak to Jock. Miguel will wish you good luck and tell you that he can make it on his own from here.

Statistics