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When you're ready for the assault on the Military Base, keep in mind you can ask a few paladins from the Brotherhood to assist for extra (hehe) support.
The Cathedral is one of your final objectives of the game. It can be done before or after the Military Base, it makes no difference since you have two main quests really form one goal: to end the mutant threats. Since the Master and the Cathedral is perhaps a more dramatic ending, it is why you've found it at the end, though it isn't any more difficult than the Base and actually can be quite a bit easier depending on how you approach it.
If for some fluke of nature the Cathedral isn't yet on your World Map, it is due south of the Bonyard two grid squares, right along the coast. Enter the first area, and click on the entrance grid to the door to be teleported inside.
Your main goal here is of course to get rid of the Master, found at Lair Level 3 (or the 3rd level of the Vault). I shall give you two options for doing that when the time comes, a brute force approach and a sympathetic ear approach.
- Entrance: the first place you enter. Enter through the doors to the Cathedral
- Tower Level 1: the main floor of the Cathedral. Laura, a possible contact is here
- Tower Level 2: super mutants on this small upstairs floor
- Tower Level 3: super mutants on this small upstairs floor
- Tower Level 4: Morpheus resides here in his room, holds the black CoC badge
- Lair Level 1: 1st level of the vault
- Lair Level 2: 2nd level of the vault
- Lair Level 3: 3rd level of the vault & the Master
- Lair Level 4: 4th level of the vault & the nuclear device
Here is a list of the significant quests in the Cathedral, each with a brief synopsis containing at least one way to solve it. The remaining ways, and possibly other minor quests I will leave up to you.
Since your main goal is to get to the Master, you should first find a way past the northeastern most door, which is locked. There are several ways. One is to lockpick it. Another is to first go to Nicole in the Boneyard Library area, and ask her about the Cathedral. She'll point you to Laura and give you a secret code word. Find Laura in a southwest room, and she'll lead you to a private area where you can talk. Then she'll proceed to unlock the door in question. Finally, you can barter the appropriate red CoC badge off either Sister Francis or Ton.
Once through the door, you'll notice another door behind the back wall of the Cathedral. This door requires a black CoC badge or a very high lockpick skill. Only Morpheus has the black CoC badge and he's on Tower Level 4, three levels up. Take the stairs to reach level 2. If you find super mutant resistance, eliminate them. The same goes for level 3. On level 4, Morpheus is in the southeastern room. Wear the robes and talk to him if you wish. If you want, you can reveal your identity and he will offer to take you to the Master. You may wish to do this if you want to avoid combat, but otherwise kill him, take his black badge and you'll get 1000xp. In the room next door you'll find some Tesla armor in the locker.
Make it to Lair Level 3 (Vault Level 3):
When you have the black CoC badge from Morpheus (see above), head downstairs through the door on the 1st level down to Lair Level 1, which is really Vault Level 1. There is a secret passage near the southeastern most bookcase. If you wait a minute or two, Jeremiah will come walking through the passage and question you. Prepare for a short fight. It is possible to bluff him out of attacking as well, just make sure to wear robes for these attempts. Another alternative is to use your Lockpick or Traps skill on the bookcase to reveal a lever. Then use the bookcase to open the secret passage. Finally, you may blow up the entrance using dynamite.
There are nasty creatures on your way to the elevator of the vault, and two guards. Bluff your way past them for 750xp (while wearing the robes) and head for the elevator. You'll see a computer near the elevator. Use your Science skill on it to reveal the location of the secret Military Base (even though you should have it) and you'll receive 1250xp.
Take the elevator to level 2. In the northwestern most room you'll find Gideon. Speak his own double-talk with him for awhile for 1000xp and the Psychic Nullifier, an item needed if you want to remain unaffected from permanent damage on Level 3. All of the occupants of the room have one if you would rather steal it.
In the southern room of level 2 you'll find a console. You can use it to "free" the prisoners for 2000xp. Proceed now to level 3 and I'll present your options for ending the game (if you've already destroyed the Military Base).
There are two ways of dealing with the Master face to face, and a way of blowing up the whole Cathedral, which kills everyone except you, as you'll escape before the timer runs out. For arming the nuke and starting the countdown, see below. For dealing with the Master personally, read the quest after.
Arm the Nuclear Bomb:
Before starting this, you must have the key from the Military Base or a decent Science and Repair skill (70%+) to succeed. In the west room of level 3, there are several super mutants. Kill them if you wish (who will be aided by weak CoC members) and attempt to unlock the elevator door. Proceed down to level 4 and into the room with the two super mutants, a console and a nuclear bomb. If you touch the computer, you will anger the two guards who will then attack, but there is no way around this. Kill them, and either use the key from the Military Base level 4, or first use Science and then Repair. When you are successful, you'll have 240 seconds to escape. Equip your robes for a fast exit. Now witness the end of game sequence and your last conversation with the Overseer of Vault 13 if you've destroyed the Military Base. Congratulations.
Confront the Master:
Kill the enemies on level 3 if you wish first, or simply walk to the southeast section of the level with your purple CoC robes on undisturbed. If you do not yet have the Psychic Nullifier, be sure to get one on level 2 from Gideon or steal one from any of the people in that room. Equip it in an active slot and look for a doorway attached to the righthand side of the southeastern room. Open it up and take the obscene hallway toward the Master. Make sure that you are healed, weapons loaded and ready for a fight, if it ends that way.
As I said before there are at least two ways to deal with him. You can take the diplomatic or violent approach. The only difference is suicide versus homicide. For the diplomatic approach, you'll be needing the mutant experimental holodisc from Vree at the Brotherhood of Steel for "proof." That and a high speech skill. Since the conversation path is fairly complicated, I will paraphrase it in detail here:
Master: Ha, you pathetic human. We represent the best hope for humanity.
You: Prove it.
Master: I don't have to.
You: I can't know you represent the best hope until you prove it.
Master: Very demanding, but I respect you... maybe more than you'll ever know.
You: So tell me then!
Master: Yadda yadda.
You: That race being the mutants, of course.
Master: Yes, blah yadda blah.
You: You mean to change all the others into mutants, dontcha punk.
Master: Yes, yadda blah.
You: For such a smart mutie, you've got a problem with your master plan.
You: I happen to know all muties are sterile.
Master: Say what?
You: Oh, you boys may not have been sterile before, but now... you reek of sterility.
Master: Prove it.
You: Of course. (show him the holodisk from Vree)
Master: Must compute this. It is a forgery!
You: Nonsense! You're only denying the facts I laid out for you.
Master: Then I am a failure.
You: Sorry to be the bearer of bad news, but your plan could never work. Your race will die out after this generation.
Master: Go. Just go...
The End. Queue 240 second countdown.
And the other (more likely) option is to kill him. He's got 500hp but nothing a few critical hits with your favorite weapon can withstand. One good tactic is to use the pillars for cover. Step just one hex behind one for the Master's turn. When it is your turn, take one step out, fire, and one step back behind the pillar. Another is to simply aim for his "eyes" and hope for critical hits. This can be even more effective if you have an excellent critical chance, the "better crits" perk, and good marksmanship. Either way, when he is dead you'll have 240 seconds to escape. Put on your robes and flee if you want to make it out fast. When you've reached the World Map, you'll be treated to the ending, and a brief final conversation with the Overseer of Vault 13, if you have already destroyed the Military Base. A very big congratulations for completing the game!