In "Fallout," the Master is the final boss of the main storyline. The Master battle is hard, requiring high health and several helpers... if you actually fight him, that is. With enough intelligence, speech and the right items, you can completely avoid this battle by revealing a fatal flaw in the Master's plan -- one that causes him to destroy himself.
Smarts Pay Off
For this ending, you have to be smart and silver-tongued. Your Intelligence stat has to be at least 8 and combined with a very high Speech skill to guarantee success. You can raise your Intelligence by 1 via surgery from the Brotherhood of Steel doctor in Lost Hills. The Smooth Talker perk also raises your Intelligence by 1 for conversations only. You can also pop a Mentats before talking to the Master to raise your intelligence by 2.
Right Tools for the Job
You'll need Robes to pull this off. Robes can be looted from Children of the Cathedral, found on the floor at the Boneyard base of the Followers of the Apocalypse and found in a locked room in the Children's Hospital in The Hub. You'll also need Vree's autopsy report, which Vree gives you at Lost Hills as part of the quest "Destroy the Mutant Leader."
To access the Master, find the man in leather armor in the main prayer area of the Cathedral and barter the Red COC Badge from him. Use the key to unlock the door next to a woman in a leather jacket and find Morpheus. Kill him or wear the robes and persuade him to give you the Black COC Badge. The Cathedral basement has a hidden door to the vault where the Master waits. You can fight your way to the Master or use your Robes and Speech skills to diplomatically bypass enemies. If you don't kill the enemies on the way, you will have to on the way out -- they will always be hostile when the Master is dead.
The Fateful Conversation
Before speaking to the Master, equip your Robes and if necessary pop some Mentats. If you haven't read the autopsy report yet, do so. Then, talk to him and select the following dialogue choices as they appear:
"If you can prove to me that your Unity is the best course for Humanity, then I will help you." "I can't know you represent the best future unless you prove it to me." "So tell me." "That race being mutants, of course." "You mean to change others into mutants, as well." "You've got a problem with your master plan." "I happen to know your mutants are sterile." "Have you talked to any of your mutants about this?" "How about a female mutant?" "Sorry, your race is doomed." "Sorry this isn't an option for you...race...die."
The Master will give a final speech, at which point you should immediately leave the Cathedral -- the whole place is being nuked in four minutes, you included if you're still inside.