I believe they forced the coads out of him then used them to sistymaticly(spelling error lol) destroy the world!!!
or possibly...... the enclaves real plan to ride out a nueclear war was in a giant spaceship(i read that in the wiki) could it be posible that the plan sucededI(they would do this when nueclear tensions were at there highest)? but that aliens took the ship and forced the(high ranking) people inside and forced them to give them the codes? then they used those codes to destroy thw world
Also in one of the rooms in Zeta you can find several barrels (like the ones scattered across the wasteland in DC) in a tube. could they have possibly spread radiation across the DC because the nukes there were programmed not to strike whithin 10000 yards (or something) to prevent terrorists hacking there systems and they needed to destroy the capital.(which would explain the small amount of structural damage that has been bugging me)
Now if u just bought the game then there are no mutant overlords but after u get broken steal they add them in. There are several super mutant overlords frozen in Zeta.(which you can unfreeze) this makes me think whether or not they created the incredibly strong mutants. That also makes me think. super mutants are made by throwing humans into bats or FEV(forced evolution virus) in the DC there breeding ground is vault 87. A super mutant behometh would NOT be able to fit in the vault. maybe the aliens created them.
There is a larger amount of super mutants in DC then anywhere else in fallout history (except maybe near the masters citadel) and that is the place the nukes were evidently kept. it seems to me as though they used the giddy up horses(or whatever theyare called) to disable security systems making hacking Americas icbm system easier. But they couldnt nuke DC itself due to some subroutine or something.So they created loads of super mutants. (maybe they gave vault tec the FEV virus to creat mutants for them)