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Yes and no, they seem to have organized groups and occupy territory together, but there is no known official governing system or overall rulers such as a King or Queen. Many NPCs often mention that the Super Mutants seem to be looking for something, but as far as I know, nobody ever clarifies what it is they are looking for. A social class also seems to be present with regular Super Mutants, Brutes, Masters, and Behemoths(if you consider them a type of Super Mutant). If you play through the main quest, you will eventually stumble upon clues of how the Super Mutants came to be as well as how they are discriminant to certain members of their kind, like those who have intelligence or a good disposition to humans.