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“Let those who would disturb her sleep fall into the depths of endless darkness...”
Dark Bones are the most powerful type of Dry Bones. Instead of being a pale gray with red shoes, they are a bluish violet with purple shoes. Dark Bones are only found in the Palace of Shadow (where they are seen twice, once in a corridor and yet again in Riddle Tower) in Paper Mario: The Thousand-Year Door. Showstopper, the special move, can actually destroy the Dark Bones.
It is unknown whether Dark Bones affiliate with Bowser or not, but they appear to be affiliated with the Shadow Queen. However, a certain Dark Bones's pre-battle speech seems to indicate that it has been ordered to keep the Shadow Queen from awakening.
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