Driving back from a washout fishing trip, the gang takes a shortcut through a dismal swamp, where they meet up with a spooky zombie. Coming to the deserted town of Swamp's End, they learn that the zombie was conjured up by a bayou witch. Now only two people are left in town: the store owner Zeke and his cousin Zeb. While Freddy and the girls stay at the store to clean up a mess that Scooby has made, Shaggy and Scooby go off to Zeb's shack to question him. He isn't there, however; all that is left of him, it appears, is a voodoo doll in his bed.The gang go into the swamp and find the witch's house, which contains voodoo dolls resembling the four kids. The witch appears and causes Daphne to disappear before she herself vanishes in a puff of smoke and flame. But it is a trick, as the other members of the gang deduce that Daphne was pulled down in a trapdoor. Following footprints that lead away from the witch's house, they find an abandoned riverboat. Shaggy and Scooby find the zombie in a deckbox; it chases them into the abandoned riverboat saloon, but they manage to lose it. Meanwhile, Fred and Velma find Daphne tied up in a bulkhead; a winch, some power tools, and cutting torch are also stored there. The witch, flying through the air, appears and chases them down a coal chute.
Fleeing the witch and zombie, Shaggy and Scooby crash through the deck and into an airboat, where they rendevouz with Freddy and the girls. They escape the riverboat in the airboat, and when they try to stop by tossing out the boat's anchor they drag up a sunken armored truck (still loaded with money) out of the swamp. The gang uses the money and truck to trap the witch and zombie, who are unmasked as Zeb and Zeke. The pair had hijacked the truck years before and sunk it in the swamp. When they went to retrieve it, however, they couldn't find it, and used the witch and zombie act to scare people off while they searched for it.