In Fo1, the plot was Super Mutants where making more of them by "dipping" and the Master was, oh I forgot his name (Mark?? lol), an Apocalypse dude siding with the smarter one out of the Super Mutant group (David??) and they just wanted to make everyone Super Mutants right??
Sorta. The Master, AKA Richard Gray, aka "The man with enough tentacles to star in a hentai movie" found FEV and decided to start dipping people because he believed that Mutants were a form of life better suited to survive in the wasteland.
To facilitate this, he formed a group of human cultists, the Children of the Cathedral, who functioned as his spies. Since a super mutant is rather obvious.
What I don't get is why aren't they in Fo3 really.
Because the Vault Dweller stopped them more than a hundred and twenty years ago. Also because the super mutants in Fallout 3, besides being a different color, are also stupid. Far too stupid to actually conceive of such complicated plans as "infiltrate your enemy" and the like.
There's no reason why they wouldn't be...or no?? That and the Apocalypse were like the Power of Atom on that game. How did they change so much from the first game to now??
No. The Church of Atom in Fallout 3 is a totally Bethesdan-invented religion, which is probably part of the reason it was so stupid. At least the nuke-worshipping religion in Fallout Tactics was composed of Ghouls descended from original silo personnel.
There's no relation between the Cult of Atom and the Children of the Cathedral. Nor is there any between the CoA and the Followers of the Apocalypse.
They did not migrate east. As I said, the East Coast mutants have no connection to the Master or his army.
Well, they did move eastwards, they just didn't get much farther than the Mojave. (Or St. Louis if you take Tactics as canon.)