After a fishing trip, the gang gets lost in a swamp. They ask for directions from a man standing at the side of the road. The man turns out to be a...zombie! They drive to Swamp's End, an abandoned village, where they meet store owner Zeb and his cousin Zeke, the only two people left in the village. Zeb and Zeke tell the gang that the zombie was made by a bayou witch. While the gang stays back to clean up a mess Scooby has made, Shaggy and Scooby go to Zeb's house to question him. Zeb is not home, but they find a voodoo doll in his bed.
The gang follows the witch and zombie to the witch's house and find voodoo dolls of themselves. The witch appears and causes Daphne to disappear and then she herself disappears in a puff of smoke and flame. Investigating the spot where Daphne was standing, the gang deduces that she fell through a trapdoor. Shaggy and Scooby find the zombie in a deckbox, but loses him after going into an abandoned riverboat saloon.
Meanwhile, Fred and Velma find Daphne tied up in a bulkhead where 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 stop the airboat 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, they couldn't find it, and used the witch and zombie act to scare people away while they searched for it.