Destroy the Mutant Leader

Destroy the Mutant leader is a main quest in Fallout.

Quick walkthrough

 * Go to the Cathedral.
 * Obtain a red COC badge, head upstairs and kill Morpheus for his black COC badge.
 * Get into the basement.
 * Go through the hidden bookcase door.
 * Go through the Vault to the third floor.
 * Deal with the Master.

Detailed 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 seemingly peaceful Children of the Cathedral have, up until this point, been a helpful, if not irritable group, with their free hospitals in Junktown, Necropolis, and the Hub. Now, you'll need to enter their Cathedral's walls and discover and defeat the evil contained within.

The Cathedral is located two squares south of the Boneyard, and with only Katja being able to mark it on your map, you'll need to go looking. Once you arrive, you need to go through a staircase in the back of the main room. However, the door leading to that room is locked. To get there, you need a red COC badge. Most of the Children in the main room, like Lasher, will carry one.

Once you get to the stairwell, you need to go down it. However, another locked door blocks your path. To get past that one, you need Morpheus' black COC badge. Head up the stairs nearby, Morpheus is on the third floor. Blast him. He's worth 1000 XP, and you can grab the badge off his corpse. The nightkin you passed on your way up will actively shoot you up, so kill them too.

Once you go down the hidden staircase, you'll find yourself in a dead-end library. Search the wall on the east side to find some intricate grooves. Use lockpick on the nearby bookcases to find a lever and open a hidden passage. If it's after 8 P.M., there will be a Centaur and two Floaters out in the caves, along with two armed super mutants regardless of the time.

Enter the LA Vault. The first level is home to several more super mutants, so fight your way to the elevator. Your destination is the third floor. Hit the button.

Once you get there, you'll be attacked by several Mister Handys, floating eyes, and super mutants. Kill them, then head down the corridor to where the Overseer's chair would be.

As you walk down the corridor, you'll get progressively worse messages in the message box. You'll also take eye damage and lose 2 points of Perception and Intelligence each by the time you reach the far side. You can evade this by taking the Mental Block perk, or taking a psychic nullifier from one of the psykers on the 2nd level. At the very end lies the Master.

Combat solution
He's a very powerful foe, with twin Gatling guns, and support from two floating eyes and a contingent of super mutants, but by now you should be a force to be reckoned with. Turn him into gooey paste for 10,000 combat XP which is likely to level you up. Wait until you are clear of the Cathedral first though as once you have killed the Master the entire thing goes into a self destruct sequence.

If you are having some trouble killing the Master, and particularly if all your team has died by this point, forgo the dialogue and use one of the two pillars for cover to shoot out the eyes and mutant in-between shots at the Master. Once he explodes, use all the firepower you have to finish off anything else and run like hell (remember that timer). If you don't make it out in time then you die. (And make sure you leave the map like when you blow up Mariposa, simply being 'outside' the building won't count).

Speech solution
If you can't kill the Master in combat, you could also talk him out of his plans for the Unity. You either need a very high Speech skill, or Vree's autopsy report. Once you read the holodisk, you can show the Master that all mutants are sterile. He will be unable to cope with the things he did in the name of the Unity, which he now knows to be all in vain, and he will tell you to leave him alone, and find safe ground. He will commit suicide by detonating a nuke beneath the Cathedral.

Nuke solution
That same nuke can also be used by you, if you have the Lieutenant's key from Mariposa Military Base. Get to the third level, but take a left when you get to the intersection. There will be be a few more super mutants, and an elevator behind them. Enter that elevator and use the key to set the nuke for a 4 minute countdown. If you're still on the Cathedral map when she goes up, you do too.

Rewards

 * 10000 XP for killing the Master (plus combat experience)
 * Ending, if you first completed the Destroy the source of the Mutants quest