I would say that it really depends on the base, would Prime expand outside? IMO the answer is no, it is THE command base for the Project! This is perhaps the single greatest issue with the Prime Base module, the abandonment of its primary mission in favor of a "feel good" operation that ultimately backfired.
So the command bases would stay concealed for some time, as would the regional supply bases.
Commo bases? By their very nature, they would be exposed to anyone with the ability to triangulate their location. I feel these bases, as written, were not really thought out very well. But then what form would these bases take?
Agriculture bases, would almost certainly go "public", as soon as they awakened, especially so that they can best use their stocks of seeds, animals and tools.
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The reason that the American Army does so well in wartime, is that war is chaos, and the American Army practices chaos on a daily basis.
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