Comedy, Thriller, Mystery, Horror, Family, Animation, Adventure
Scooby and the gang visit Zombie Island, where they find themselves menaced by the ghost of Moonscar...
The movie opens with Mystery Inc. being pursued by a green troll. After an accident with Scooby, he is caught and revealed to be a counterfeiter. This is actually a re-enactment of the now-dissolved Mystery Inc.'s adventures on a television program by Daphne and Fred, who are running a successful TV series (Coast to Coast with Daphne Blake). Velma has gone on and become the propietor of a mystery bookstore, and Scooby and Shaggy bounce from job to job, including working in customs at an airport, from which they are fired after eating all the confiscated imported foods. Since their mysteries have all involved mere crooks in monster costumes, Fred decides that Daphne's show should be about tracking down real ghosts, so he gets the gang back together for a trip to Louisiana.
After encountering a lot of fake monsters, like a nerdy guy in a lobster-man suit haunting a fish factory, an old man disguised as a gargoyle, a holographic ghost and a zombie policeman that turns out to be a woman, the gang finally arrives in New Orleans. There they are invited by a young woman named Lena to visit Moonscar Island, the home of her employer, which is allegedly haunted by the ghost of the pirate Morgan Moonscar. Although the gang is skeptical (except for Shaggy and Scooby), they decide to go with Lena, on whom Fred has taken a fancy. On the way, Velma informs the gang that Moonscar Island has had many unexplained disappearances over the years.
On the island, the gang meets Lena's employer, Simone Lenoir, a beautiful French-American; Jacques, the island's ferryman; and Beau, Simone's gardener, to whom Daphne takes a fancy (to Fred's disapproval). They also meet Snakebite Scruggs, a grungy fisherman, and his hunting pig, Mojo. The first act is like a standard Scooby-Doo cartoon, with the gang investigating and working to prove that the "ghost" is fake. Scooby and Shaggy are chased by Mojo and end up falling into a big hole. While trying to climb out, they pull down some of the wall, revealing a skeletal arm. A mysterious green fog envelopes the skeleton, causing it to transform into the grisly zombie of Morgan Moonscar himself. While running away, Scooby and Shaggy run into a suspicious Beau and bring everyone back to the hole, which is now, however, empty.
Simone invites the gang to her house to stay for the night. As the gang is dressing up for dinner, Shaggy sees the ghost of a Confederate colonel in the mirror; Simone explains that the island was a temporary headquarters for a Confederate regiment during the American Civil War. Later that night, Scooby and Shaggy eat in the Mystery Machine, so Scooby wouldn't chase Simone's cats. However, they burn their mouths on the spicy food, and both of them rush to the lake for water. The green fog reappears and sinks into the nearby ground, causing an army of zombies to emerge from the lake. Due to Shaggy's bad driving, the Mystery Machine gets stuck in a muddy bank, forcing him and Scooby to flee on foot. Fred, Daphne and Velma go to look for them, but bump into Beau, so they split up.
Fred and Daphne argue about each other's supposed love interest. They come across Scooby and Shaggy trying to escape, and they also capture a zombie. Fred thinks the zombie is another fake, but it turns out to be all too real, and when the other zombies begin to swarm them, Scooby, Shaggy, Fred and Daphne separate in panic. Fred trips on a stone, and his camera (which he used to record their investigation) sinks into quicksand. Fred and Daphne reunite with Velma and Beau (Velma is now suspicious of Beau because "he is never nearby when something strange happens" and she decides to stick by him). Scooby and Shaggy discover wax dolls that look like Fred, Velma and Daphne, and they play with them, causing his friends to undertake a series of involuntary actions for a short time.
Fred, Daphne, Velma and Beau return to Simone's house and discover a secret passage under the staircase. They find Lena in the passage, who tells them zombies kidnapped Simone and dragged her away. Daphne, Fred, Velma, Lena and Beau proceed down the passage and find a secret chamber, where Velma finds Simone's footprints (meaning she wasn't "dragged") and questions Lena about the story. Indeed, Simone appears, and she and Lena use voodoo dolls to trap the gang in the chamber. They show themselves to be evil werecats, and Simone reveals that in the 18th century, she and Lena were part of a group of settlers who made the island their home. One night, during the harvest moon, while the settlers were celebrating their successful harvest, Morgan Moonscar and his pirates chased the settlers, except for Lena and Simone, into the bayou where they were eaten by alligators. A vengeful Lena and Simone begged their cat god to curse the pirates. Their wish was granted, and they killed the pirates, but the curse caused them to become werecats permanently, requiring that they drain life forces to preserve their immortality. Over the years Lena lured more people to the island, and they also gave Jacques immortality so they had a ferryman to bring them more victims. The zombies - including Morgan Moonscar - were the victims they have murdered over the centuries, who reanimate every harvest moon to warn away visitors.
Scooby and Shaggy accidentally tumble into the cave, interrupting the draining ceremony and disctracting the werecats. Velma is quickly able to untie herself and create voodoo dolls of Lena and Simone to interrupt their power. When they are finally cornered, the werecats' curse expires, causing their bodies to age hundreds of years and disintegrate, freeing the zombies' souls to rest in peace. Afterward Beau is revealed to be an undercover police officer sent to investigate the disappearances on the island (to Velma's fascination); Fred and Daphne become a couple again, and Daphne offers Beau a chance to guest-star on her show and discuss the adventure.