Destroy the source of the Mutants

 is the penultimate quest in Fallout.

Walkthrough
You've trekked across the wasteland and brought the Water Chip back to Vault 13, but the mutant armies pose a dangerous threat to the safety of the Vault populace. You must stop their mad leader, and destroy whatever is creating them.

The supermutants have proved to be formidable foes thus far, and now you need to do something about them. Enter their secluded hideout, and purge the FEV they're using on the people of the wasteland.

Find the base
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 chainguns, laser rifles, and rocket launchers. They'll also usually have a few Centaurs or Floaters for pets.

Once you finally find the massive installation, you'll need to get inside. There are four mutants outside the base, 3 with laser rifles, one with a rocket launcher. You can use a Radio to draw the launcher and two of the riflemen away from the base, and earn 1500 XP for tricking the stupid lugs. The mutant who doesn't leave holds a tape that contains the door code to the base's entrance. Enter the main base.

Inside the realm of nightmares
Once inside, you'll immediatly trigger the alarm and mutants will open fire on you. There are four that come running, two with miniguns, two with rocket launchers. Kill them, then check out the force fields. The yellow ones can be shut down for a minute by using Repair on their emitters, while you can run through the red ones and take a little damage.

There's a computer console behind a few yellow fields that you can hack to take control of the base's security systems. You can alter the robots' programming, and set your radio's frequency to that of the emitters to shut them down remotely. Tampering with the robots will make them friendly, and changing the pest control to "large pests" will kill three mutants on the second level. Then, head to the elevator

The deadliest game
While the second level holds plenty of loots, the third level is where you want to go. You'll come across a big, suspiciously empty room. If your Traps skill is high enough, you'll find all sorts of landmines and tripwires in there. Get to the yellow field at the end of the hall, and blast the two mutants there; Krupper and Flip. Go down the next elevator.

Heading to the left will produce an encounter with Vat Team 9, a crack squad of mutant soldiers, while the right leads to the Lieutenant and VanHagan of the Children. Head to the right. If you're here without being in the company of another mutant, like Flip or Harry, the Lou will shoot on sight. He's armed with a powerful L30 Gatling Laser and a bulky 310 HP, while VanHagan will snipe away with his Glock 86. If you're being dragged by a mutie, the Lou will interrogate and torture you, then lock you up on level 3. Kill him and VanHagan, snag his key, then get past Vat Team 9.

The Vats
Go down the hallway past Vat Team 9's quarters, and enter the room with all the COC techies. One will ask if you'd shoot an unarmed man like himself, so melt him and grab his keycard. Use the terminal in the center of the overlook room to set the base to self-destruct. If your Science isn't high enough to decrypt the gibberish the terminal gives you, just pick the second one from the bottom. It has the highest timer, and won't turn all of the live forcefields into red fields.

Then, run! Get clear of the base's map.

Brothers help brothers
If you managed to convince the Elders of the Brotherhood of Steel to help attack Mariposa, there will be three Crack Assault Paladins waiting on the map. Each is wearing T-51b Power Armor, one has a CZ-53 Personal Minigun, one has an L30 Gatling Laser, and one has a Rocket Launcher. They will follow you around the exterior and blast the four mutants away, but they won't enter the base, which limits their usefulness.

Secret Agent Man
If you're wearing some Robes when you walk into the outer Military Base map, you can trick the mutants and get in without triggering the alarm. That'll let you sneak down to the control room and blow it to pieces without wasting a single round of your favourite ammo. The Lieutenant, though, can see through your disguise if you talk to him, so don't.

Reward

 * At least 10000 XP for blowing up the base.
 * The ending, if you've also completed Destroy the Mutant leader