So if you want to know how they ruined the lore, I would say that was the biggest error. That would be a much more plausible scenario. So if Bethesda wanted to bring them back, they should have had them come from a military base that was working with the laboratories on the west coast at the time and shared data. Not to mention the FEV labs were supposedly destroyed at the end of FO1.

Not to mention they would not have to worry about the backlash once the vault opens after the experiment and people find out that one of vault-techs highly publicised vaults has somehow become infested with super mutants. They could conduct the experiment themselves and have fewer security leaks as a result. In fact the miliary has no reason to involve vault-tech in any way. Instead the military would test it on volunteers, military volunteers who had clearance, in order to minimize the public backlash. There is no logical way that a private industry would get access to a top secret military weapon for the purposes of testing it on unwilling civilians. Moreover even if they did, the FEV is a weapon created by the US military to create front line soldiers. However they did not run social experiments like subliminal messages or exposing people to the FEV to make super mutants. Kudos to Bethesda for using it correctly in the plot by the way. So they made things along that line, like the GECK which contains blue prints and materials necessary to rebuild society once the vault opens. Although they did have impressive tech, that tech was related to these vaults, for example power generating and water purification plants.

Vault-tech made their business form building massive massive fallout shelters and selling space inside them, taking advantage of the fear of nuclear war. The worse way that Bethesda ruined the lore was that all of the super mutants in FO3 came from a vault-tec facility. In F3, they all come from the SAME single place, so naturally regard each other as allies.ДЄs for where these factions stand in F4? NO ONE KNOWS. FNV's are only 'organised' in that they've established some communities. While the Outcasts are indeed closer to their 'roots', the very fact that Bethesda INCLUDED that schism is a nod to the prior lore: they establish that Lyons is taking his Capitol Brotherhood in a direction different from prior BOS history.ДЄnd, the supermutants? In both F3 and FNV, they are not organised to speak of. They let actual _ghouls_ become Initiates. The Brotherhood has not always acted as elitist as the Outcasts - Midwestern Brotherhood, in Tactics, for example. It's not unreasonable to posit they had other bases elsewhere (after all, they would have to have somewhere to support the population needed to maintain their technological and industrial base, in order to field an actual army) - and after a time of confusion due to loss of command-and-control, would recover, and formulate new plans. Even in F2, they didn't do that they had the Oil Rig, yes. The thing with a conspiracy like the Enclave is: they never, ever, ever put all their eggs in just one basket.

The Brotherhood should act like the BoS Outcasts and should also be nearly wiped out after the NCR wars and the mutant army should be no where near as organised or powerful as they are. The Enclave should have been wiped out from Fallout 2 when The Chosen One destroyed them. House:Fallout 3 included a strong presence of Brotherhood of Steel and Enclave, in addtion to supermutant army.

Secret military base fallout 4