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If you 'join' either of them, that will make the other faction hostile. The miltary - better kill them, just for fun, military medkits and Eastern ammo :) The Scientists buy artifacts at good prices and sell/give the best non-exoskeleton armor in the game.
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From Freedom you get NATO AP ammo (great down the way), but from Duty better armor, a Vintorez and ammo for it (AP included).
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You can be friends with one of them (or all, except Monolith, with Complete mod) and take missions from them.
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