What's more surprising: The existence of civilized Mutants or that they want you to eliminate other Mutants? This unusual, repeatable Minutemen recruitment quest can be found by speaking with Preston Garvey. We found that he typically doesn't assign this until you have at least a half dozen other Minutemen side quests under your belt.
When you can pursue this mission, head to the randomly designated settlement. Speak to the Mutant settler for the exact location of the nearby Super Mutants he wants killed. Head over there, wipe out the Super Mutants and head back to the settlement to report your success. Then speak with Preston Garvey to complete the quest.