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A slime mutant that lives underneath Crystal Cove is cocooning anyone who gets in its way. Despite being warned not to continue investigating by their parents and authority figures, the gang attempts to solve the mystery. Meanwhile, Velma is trying to get Shaggy to be more intimate in their secret relationship. Daphne also keeps hinting her romantic feelings towards Fred who is oblivious to almost everything apart from solving mysteries and building traps. After solving the mystery the gang comes into contact with a mysterious man who refers to himself as "Mr. E" and remarks that they have uncovered "a truth that should have remained buried" and that "the real mystery has just begun".

Overarching Mystery Clues: A locket shaped like a magnifying glass found in the Crystal Cove caves and a call from Mr. E. Villain: The Slime Mutant/Professor Emmanuel Raffalo

Note: The Black Knight, Miner 49er, Captain Cutler, Space Kook, and Charlie the Robot from the original Scooby-Doo, Where Are You! series make cameo appearances in the Haunted Museum as statues.

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