Destroy the Mutant Leader

Destroy the Mutant leader is a main quest in Fallout.

The player 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 player to stop their mad leader, The Master, and destroy whatever is creating them.

Quick walkthrough

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

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 and 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 player 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 player needs to go down it. However, another locked door blocks the path. Head up the stairs nearby, Morpheus is on the third floor. He can be killed for 1000 XP, and the black COC badge. The nightkin along the way up will become hostile towards the player.

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. Using lockpick on the nearby bookcases will reveal 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 hostile super mutants the player will have to defeat to reach the elevator to get to the third floor.

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

As the player walks down the corridor, he'll get progressively worse messages in the message box. He'll also take eye damage and lose 2 points of Perception and Intelligence each by the time he reaches the far side. 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 Gatling lasers, and support from two floating eyes and a contingent of super mutants, but by now your player should be a force to be reckoned with. Turn him into gooey paste for 10000 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 the player is having some trouble killing the Master, and particularly if all the players 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 the player character has left to finish off anything else and run like hell, (remember that timer). If the player does not make it out in time, they will die. As when the player blew up Mariposa, make sure to leave the map; simply being outside the building won't count as having escaped, and the player will die.

Speech Solution
If the Vault Dweller doesn't want to kill the Master in combat, he can also talk him out of his plans for the Unity. The player can either have him leave with the use of a very high Speech skill, or Vree's autopsy report. Once you read the holodisk, the player 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 you to leave him alone and to find safe ground. He will commit suicide by detonating a nuke beneath the Cathedral.

Nuke Solution
If the player 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 player. 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 player is still on the Cathedral map when it goes up, they go with it.

Rewards

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

Behind the scenes

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