From the Super Mario Wiki
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Black chests each contain one of the heroes that helped to defeat the Shadow Queen 1000 years ago in Paper Mario: The Thousand-Year Door. There are four in total. The heroes are now Black Chest Demons and curse Mario when opened. The "curses" are actually helpful abilities that allow Mario to access new areas. The Chests are located in Hooktail Castle, Rogueport Sewers, Twilight Town, and Pirate's Grotto. Mario can open the chests with Black Keys.
The chests are in the spot where the heroes left their Crystal Stars, since letting go of a star would trap each of them in a chest.