Destroy the Mutant Leader

Destroy the Mutant leader is a main quest in Fallout.

The Vault Dweller has trekked across the Wasteland and brought the water chip back to Vault 13, but the mutant armies still pose a dangerous threat to the safety of the vault populace. It is up to the Vault Dweller to stop their mad leader, the Master, and destroy whatever is creating them.

Detailed walkthrough
The seemingly peaceful Children of the Cathedral have, up until this point, been a helpful (if irritable) organization, with their free hospitals in Junktown, Necropolis, and the Hub. Now, the Vault Dweller needs to enter the Cathedral's walls to discover and defeat the evil contained within.

The Cathedral is located two squares south of the Boneyard, and with Katja being the only person able to mark it on the Vault Dweller's map, the Vault Dweller may need to search to find it. Once there, go through a staircase in the back of the main room. However, the door leading to that room is locked. To get there, a red COC badge must be obtained. Most of the Children in the main room, like Lasher, will carry one.

Once the stairwell is reached, the Vault Dweller needs to go down it. However, another locked door blocks the path. Head up the stairs nearby, Morpheus is on the third floor. The nightkin along the way up will be hostile to the Vault Dweller, unless they are wearing Robes, are unarmed and alone. Morpheus' death awards 1000 XP, and the black COC badge. Alternatively he can be talked into taking the Vault Dweller directly to the Master (see Speech solution).

At the bottom of the hidden staircase, there is what appears to be a dead-end library. Searching the wall on the East side will reveal some intricate grooves. Lockpick or search the nearby bookcases for traps to reveal a lever and open a hidden passage. If it is 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 hostile super mutants the Vault Dweller will have to defeat to reach the elevator to get to the third floor.

Once there, the Vault Dweller is attacked by several Mister Handies, floating eye bots, and super mutants. These must be defeated before heading down the corridor to where the Overseer's chair would be.

As the Vault Dweller walks down the corridor, they will get progressively worse messages in the message box, as well as taking Eye Damage, losing 2 points of Perception and Intelligence each by the time the far side is reached. This can be evaded 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
The Master is a very powerful foe, with twin (although dealing damage as one) Gatling lasers, support from two floating eyes, and a contingent of super mutants, but by now the player character should be a force to be reckoned with. Turn him into gooey paste for 10,000 combat XP, which is likely to level up the Vault Dweller. Once the Master is gone, the entire Cathedral goes into a self-destruct sequence.

If the Vault Dweller is having some trouble killing the Master, and particularly if all the Vault Dweller's 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 left to finish off anything else and run like hell (remember that timer). If the Vault Dweller does not make it out in time, they will die. As when the Vault Dweller blew up Mariposa Military Base, make sure to leave the map; simply being outside the building won't count as having escaped.

Speech solution
If the Vault Dweller does not want to kill the Master in combat, he can also be talked out of his plans for the Unity. The Vault Dweller can either convince him with the use of a very high Speech skill, or Vree's autopsy report. Once they read the holodisk, the Vault Dweller 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. He will then tell them to leave 'while you still have hope' and to find safe ground. He will commit suicide by detonating a nuke beneath the Cathedral. The player character must again have a high Speech skill to use Vree's tape as proof for the Master that the mutants will fail. However, use of certain perks negates the Speech alternative, and makes this ending unavailable; even with maximum Speech level and Vree's tape.

Nuke solution
If the Vault Dweller has either the Lieutenant's key from Mariposa Military Base or a very high Science level, that same nuke may also be used by the Vault Dweller. Get to the third level, but take a left once the intersection is reached. There will 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. Be careful, if the Vault Dweller is still on the Cathedral map when it goes up, they go with it.

Rewards

 * 10000 XP for killing the Master (plus combat experience).
 * 2000 for freeing prisoners.
 * Ending, if the Vault Dweller first completed the Destroy the source of the Mutants quest.

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

Destruir al Líder de los Mutantes Уничтожить лидера мутантов