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Postan evil team idea. It combines the evil organization which has already taken over the region, and the Conquistadores/treasure hunters ideas.
This team would exercise tight control, and the player would become aware of them by talking to a resistance group who is constantly accused of being paranoid conspiracy theorists (bonus points if we give them tinfoil hats and make them talk like /pol/ posters.) Later, the player decides to assist in the effort of taking them down for good, for the sake of his family, friends, and the whole world.
If anybody has anything they'd like elaborated, please ask. I've got nothing else to do.