Destroy the source of the Mutants

Destroy the source of the Mutants is a main quest in Fallout.

Quick walkthrough

 * 1) Travel to Mariposa Military Base.
 * 2) Kill the super mutants and loot the holodisk that holds the door code. The Vault Dweller can use a radio to draw some of the guards away from the door and earn 1500 XP.
 * 3) Navigate to the first elevator. Yellow force fields can be temporarily disabled using the Repair skill in their devices, but beware, using the tool won't work. Red force fields can be traversed, though the Vault Dweller and companions will take minor damage.
 * 4) Travel to the third level.
 * 5) Move to the south elevator.
 * 6) Travel to the fourth and final level.
 * 7) Kill the Lieutenant and Van Hagan for a key to the north-west area.
 * 8) Enter the north-west area with the Children of the Cathedral followers. There is one in particular that stands in front of the console (northernmost console, facing south).
 * 9) Kill him, loot the password from his body, and access the terminal. If the Vault Dweller's Science skill is not high enough to decode the messages, select the option second from the bottom. It gives the most time and turns all yellow force fields red.
 * 10) Get out before the building blows up.

Detailed walkthrough
If the Vault Dweller enters Lost Hills and speaks to Elder of the Brotherhood located on level 4, or to Head Paladin Rhombus on level 1, they will both tell them that there are rumors of an army massing to the north.

The Military Base is located a good number of squares to the northwest of the map, far from anywhere else in the wasteland. The desert surrounding it is patrolled by Unity kill-teams, equipped with miniguns, laser rifles, and rocket launchers. They'll also usually have a few centaurs or floaters for pets.

Once the Vault Dweller finally finds the massive installation, they need to get inside. There are four mutants outside the base, 3 with laser rifles, one with a rocket launcher. The Vault Dweller can use a radio to draw the launcher and two of the riflemen away from the base, and earn 1500 XP for tricking them. The mutant who doesn't leave holds a tape that contains the door code to the base's entrance. Alternatively, Katja can also pick the lock. Enter the main base.

Combat solution
Once inside, the Vault Dweller will immediately trigger the alarm if they are not wearing robes and Mutants will open fire on sight. There are four which come running, two with miniguns, two with rocket launchers. Defeat them, then check out the force fields. The yellow ones can be shut down for a minute by using Repair on their emitters, while the red ones can be run through in exchange for a little damage.

There are two computer consoles behind a few yellow fields that can be hacked to take control of the base's security systems. The Vault Dweller can alter the robots' programming on the console near the elevator, and set his radio's frequency to match the emitters and shut them down remotely on one in the far south-eastern end of the level. Tampering with the robots will make them friendly, and changing the pest control to "large pests" will kill three mutants on the second level.

While the second level holds plenty of loot, the third level is where the Vault Dweller needs to go. They'll come across a big, suspiciously empty room. If their Traps skill is high enough, they'll find all sorts of landmines and tripwires in there. The player needs to get to the yellow field at the end of the hall, and blast the two mutants there; Krupper and Flip.

After taking another elevator down to level four, heading to the left will produce an encounter with Vat Team 9, a crack squad of mutant soldiers. To the right leads to the vats, the Lieutenant and Van Hagan of the Children.

If the Vault Dweller enters the Lou's office on his own, without being transported there by Flip or Harry, the Lou will shoot on sight. He's armed with a powerful gatling laser and a bulky 310 HP, while Van Hagan will snipe away with his laser pistol. If the Vault Dweller is dragged here by a mutant, the Lou will interrogate and torture them, then lock them up on level 3.

The encounter with the Lieutenant is entirely optional. The Vats control room is down the hallway past Vat Team 9's quarters, the room with all the COC techies. Use the terminal in the center of the overlook room to set the base to self-destruct. If the Vault Dweller's Science isn't high enough to decrypt the gibberish the terminal shows, they should pick the second one from the bottom, which sets the timer to the longest possible duration and removes yellow force fields. Alternatively, a keycard from one of the techies can be used to automatically decrypt the codes.

Afterwards, clear off to the worldmap.

Infiltration solution
If the Vault Dweller is wearing some robes when they walk into the outer Military Base map, they can trick the mutants and get in without triggering the alarm. That will let them sneak down to the control room and blow it to pieces without wasting a single round of ammunition. Another approach is using a Stealth Boy and sneak through, but keep in mind you will need a high Sneak skill and cannot walk too close to the mutants or they will detect you. The Lieutenant, though, can see through their disguise if talked to.

Rewards

 * 10000 XP for blowing up the base.
 * Ending, if the Vault Dweller has also completed the Destroy the Mutant leader quest.

Behind the scenes

 * The speech given by Jacoren at then end of this quest is referenced in Fallout 3 by Amata after the Trouble on the Homefront quest.

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