You can simply kill them all. Or try other options.
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 convince him to stand down with the use of a very high Speech skill.
Alternatively, he can be confronted with a slightly lower Speech skill and Vree’s autopsy report. The Vault Dweller must have an Intelligence skill above six to obtain the tape from Vree. Once they read the holodisk, they 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 all be 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.
If the Vault Dweller has either the Lieutenant’s key from Mariposa Military Base or a very high Science skill, 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. Two mutants guard the nuke and once they’re taken care of, use the key to set the nuke for a four-minute countdown. Be careful, if the Vault Dweller is still on the Cathedral map when it goes up, they go with it.