Fallout 3, super mutant HQ?

there isnt a central command facility that, if destroyed will destabilize them. but they are created out of vault 87 on the far west of the map. warning you cannot directly approach the entrance as it took a direct hit from a nuclear device during the war. rads peak at 2500/second. they also essentially control downtown dc, so if you want to bring some mutie pain, head there and explore. the capitol has a constant (until you kill everyone that is) battle between talon company mercs, enclave after they are encountered and mutants both inside and outside of the facility