The group is led by Jacob the Chemist, it being paradoxical, seeing as how he was named after Marcus's best friend, Jacob, of the Brotherhood of Steel. Members include Jacob's wife Aileen, Manson, and Franc. Liz also has a hand in trying to get rid of the mutants.
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, they can break Manson and Franc out of prison and blow up the mine's air purifier. Doing the latter affects Broken Hills' ending of the game. Alternatively, to thwart the group, the Chosen can put Jacob and his wife in jail by accepting either of the quests, then reporting to Marcus, the mutant sheriff, about their plans. Doing this, or finding the people who attempted to kill Francis, will change Broken Hills' ending.
If the Chosen One helps 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 group is stopped, then Broken Hills will do well until the uranium runs out, after which it will peacefully disperse and, if still alive, Marcus will head east (this ending is canon). If nothing is done, 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 would blow up the mine and leave Broken Hills.