For more information, on how the anti-mutant conspiracy affects the ending of Fallout 2, see Fallout 2 endings.
The Chosen One has the choice between stopping or aiding the cause of the mutant conspiracy. To aid the mutant conspiracy, the player can complete two quests, Break Manson and Franc out of prison. and Blow up the mine's air purifier. Doing the latter affects Broken Hill's ending of the game. Alternatively, to thwart the group, the player can put Jacob and his wife in jail by accepting either of the quests, then warning Marcus, the mutant sheriff, about their plans. Doing this, or finding the people who attempted to kill Francis, will change Broken Hill's ending.
If the player chooses to help the group, then Broken Hills will try to thrive after the destruction of the mine. However, they will fail, and Broken Hills will eventually disperse. If the player stopped the group, than Broken Hills will do well until the uranium runs out, after which they will disperse and, if still alive, Marcus will head east (this ending is canon). If the player did nothing, then the group and other bigoted humans in the town will attack the mutants, ghouls, and non-bigoted humans. It is unknown if they win, but whoever wins will blow up the mine and leave Broken Hills.