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Hyper Goombas (and the rest of the "hyper" variations of enemies, for that matter) first appeared in Paper Mario. They live in Gusty Gulch, including the space beneath the Windy Mill. Paper Mario: The Thousand-Year Door introduced a few new "hyper" creatures. Along with that, it revealed that Hyper Goombas and their clan also live in Twilight Trail.
Hyper Goombas have the ability to raise their attack power by 6, allowing them to do a lot of damage. It is highly suggested that they are defeated before they can attack.
Paper Mario Stats and Tattle Information
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