Between the time of Roswell and the present day, that portion of US government which the tentacles of MJ12 had reached absolutely were warned of the approach of the 12th Planet, and absolutely set about trying to protect themselves in underground installations. The CIA was front and center in this regard, with the military close behind. The underground installations were deemed the best alternative of the 3 considered - isolated underground communities, sculpting and reducing the Earth's population to a select few, and riding out the cataclysms on another planet such as Mars or the Earth's dead twin. Not only did this alternative not require the CIA and military to leave their home planet with its comforts, it also avoided the steady spread of disease among the so-called undesirables which inevitably started infecting the perpetrators too.
These underground installations, when discovered, were explained away as a cold war precaution in case of nuclear attack, but a quick calculation belies that explanation. The number of people to be housed, and the amount of food and water stored, would not support the residents for the length of time it would take for radioactivity to fade. The stores would support them for days or weeks at best. Clearly these installations were meant for a short term stay, after which the residents would emerge back onto the surface to scout about for supplies. With a safe and undetectable hideout, the plan was to send out raiding parties that would come back with supplies, and disappear in front of those who might be in hot pursuit of their snatched goods. Thus the government, sworn to protect and lead the people, would instead steal from them, but as this was in the main nothing new to those planning this escape they saw no philosophical conflict in proceeding.
Today MJ12 is not looking to avoid the coming cataclysms in underground installations, as they realize these will be death traps, a fact the Service-to-Self aliens encouraging this alternative were well aware of. The underground installations are still being used, however, to house activities the military would prefer the public not be aware of.