One problem. If the Master won, there almost no way the Enclave would have been able to recover the FEV.
I have a feeling the Enclave may have found a way. Small scale-biological warfare, relentless air bombing. Something perhaps. Or maybe they would have figured out another way to wipe out the mutants.
So, FO2 would have been The Enclave vs The Master, and the hero would have been The Rig Dweller. Lol.
We'd all be rooting for the Enclave.
Makes me wonder if I should actually help the Master in Fallout 1.