Of course an interesting thought is did anyone actually expect the Prime Base to survive?
Bear with me on this.
Prime Base would have begun planning in say the 1960s and construction in the 1970s. Back in those days it was feasible to build a bunker that couldn't just be blown up by a couple of nukes. Cheyenne Mountain could take a 30 meg hit if it hit about a mile away. By the 80s most Russian nukes could be dropped within a couple of hundred meters. These included those fired from a submarine hiding off the coast of California. So Prime Base for all its amazing sophistication was as likely as not to vanish in a burst of light as soon as the end war kicked off. Perhaps mistaken by a Russian spy sat for a NORAD base or some such thing being constructed. You can't protect anything really from 30 million tonnes of TNT a couple of streets away.
As such the staff on board would probably be a bit more "second rank and disposable" than the actual key Morrow project staff. Most likely when they weren't killed within the first hours, never mind the months of the war they were delighted. It may also explain why they started saving the world so disasterously.
To beat the power of the nuke, the only real solutions were dispersal and secrecy. So like any government the Morrow project would have probably invested in disparate sites all over the place. A small regional airport with surprisingly large runways, a local hospital with a large number of speciality wards and a nearby solar farm. These sites might need some basic strenghtening and have really good air filtration systems. But mostly they would just be secret and dispersed. This can be seen in scenarios such as Starnaman.
As such Prime Base may just be a very fancy, expensive, white elephant an example of a much older version of the project. The actual Project maybe in far better shape than the players realise.
Finally why would you build the actual headquarters in the continential USA? For obvious reasons this is an option the US government wouldn't have had. But supposing the actual hq of the project were linked via dedicated land cables to regional hqs etc it could be anywhere, far from potential hits. Perhaps Antarctica or a remote Carribean island. Maybe the actual leadership is still slumbering many miles away waiting too for their signal?
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