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My group is a mix of military, NEMA, and skilled civilians surviving Chaos Earth. They've been working mostly military missions and the question of the main base came up last night. The group is considering going there because of the near-contradictory orders they've received. I'm going to draw up floor plans for the base, but it would be nice to have something akin to the Merc Company building rules to help build the other aspects of the base (personnel, supplies, vehicles, weapons, etc.)

I've found rules regarding the construction of merc companies, for building vehicles and robots, and even for building cities. Has Palladium released any rules, optional or official, for building a base?

I don't think I've seen anything like that in print from Palladium. The only things that jump up at me are:
-from 1E RT, and I'd hardly consider them "construction rules" for a base, more of a "guideline" in the REF Field Guide
-you might be able to adapt the Space Station Construction Rules in Phase World DB6
-you might also be able to adapt the City Construction Rules, maybe (its been a while since I looked at them so you might be better off from scratch)

Rifter 37 offers Super Hero base construction rules along these lines. It may serve your needs.