It's a full Moon night. Inside a museum, its curator is on his way to the exit. As he passes through some of the exhibits, it is revealed that the Mystery Inc. is doing some undercover work, in an attempt to catch a pair of Viking mummies who came back to life. He checks out the Egyptian exhibit, only to be startled by both mummies, who came out of two sarcofagaces. He nearly gets killed by both creatures, only to be stopped by Shaggy and Scooby-Doo, who throw things at them. After a pursuit through the corridors, and when Shaggy and Scooby are about to get caught by both monsters, someone who is behind a curtain is able to make both monsters fall, and consequently crash into some of the museum's artifacts. It is then revealed that the one who helped Shaggy and Scooby grabbing the monsters was none other than the famous Ben Ravencroft, a famous horror writer of whom Velma is a big fan, who then proceeds to reveal that the mummies are actually two archeologists who wanted revenge, because their funding was cut.
Afterwards, Ben explains them that he was doing some research for his upcoming novel, when he noticed that the archeologists were acting a little weird, and that he decided to find out what was going on. He then invites the whole gang to his home town of Oakhaven, so he could get to know them better. After a relaxing trip, they arrive at Oakhaven, but they find that the town has been built up by its Mayor into a tourist attraction. They find out that the Mayor decided to build a Puritan village in the 17th century. The Mayor and the town's pharmacist Mr. McKnight explain also that a ghost is haunting the not only the Puritan village, but also the town and that the ghost is the ghost of Sarah Ravencroft, Ben's ancestor, who was persecuted as a witch by the town in the 1600s. Earing this, Ben says that Sarah was actually a Wiccan who used natural herbs to heal people, and even had a diary of all her patients that Ben wants to find to prove her innocence and restablish the name of his ancestor.
While the gang hears the conversation, Scooby starts to dig and he finds what appears to be a shoe buckle, which Shaggy keeps in his pocket. The Mayor then tells them that they might be lucky and see the ghost that night, because according to him, the ghot appears every night, after the sunset. They then go to a local diner for food, owned by the friendly Jack. While Scooby and Shaggy stay in the diner, the rest of the gang goes with Ben to his house. There, they decide to go and see if the ghost really appears. But first, they stop by Jack's diner, where they find out that Shaggy and Scooby were still having lunch. They suggest them to come with them and see if the ghost shows up, to which they reply that they prefer to stay where no ghosts will appear.
Ben, Fred, Daphne, Velma, and many visitors stay out late and order to see the witch, but this one does show up. Meanwhile, Scooby and Shaggy finish eating and decide to find the gang, but on their way, they have an enconuter with three mysterious girls, who are dressed up like witches and have vampire teeth. Seeing them, the duo runs away, while the girls laugh maniacally on them. After being sure that they lost them, they stop for a moment, only to be then chased by a fireball throwing witch, who tries to burn them down to ashes. They eventually run into Ben and the gang returning home. Analysing the place where the witch attacked Scooby and Shaggy, they find some broken branches at the scene, and then start to hear music. Following it, Shaggy and Scooby recognize the girls who scared them earlier, are the same ones who are playing the music they were hearing. They then find out that they are the local goth girl rock band named the "Hex Girls", composed of the beautifuls Luna, Dusk, and Thorn, who use their young, natural beauty to entrance watchers while performing. Thorn and the other girls also reveal to be themselves fans of Ben's work. The gang themselves make them their number one suspects, and decide to investigate further. To do that, they split up; Fred and Daphne decide to follow the Hex Girls, while Velma, Ben, Shaggy and Scooby decide to explore the place where the witch first attacked the last two. Following some recent tire tracks, they end up in front of an old barnyard, from where they see the Mayor coming out, acting suspiciously. While Velma and Ben decide to check out what is inside the barnyard, Scooby and Shaggy follow the Mayor, who they suspect is hiding something. They almost get caught, but they manage to out-smart the Mayor, by using every kind of disguises and tricks they are able to come up with.
Meanwhile, Fred and Daphne are following the Hex Girls, who entered in a spooky and dark wood. Thorn suggests that they should do thier secret ritual that night, but Luna and Dusk reply that they are too tired, and that they should do it in the following day, just before the concert. Still, Thorn decides that she'll do it herself and after whishing goodnight to Dusk and Luna, they go on their seperate ways. Intrigued by that conversation, Fred and Daphne follow Thorn, hoping to discover what kind of ritual they were talking about.
At the same time, Scooby and Shaggy keep tracking down the Mayor, who is delivering a few suspicious packages to some people in town.
Inside the barnyard, Velma and Ben find a cherry picking truck with the engine still warm, and they ask themselves who would be driving it that late in the night.
Fred and Daphne, who kept following Thorn, see her doing some sort of ritual, and start to believe that the Hex Girls are really witches.
After awhile, they all get back together and Velma tells the Mayor that they have a plan to catch the witch. Fred divises a plan, which he thinks will help them capture the witch and find out who's behind the mystery. When the gang and Ben are ready to capture the witch, the Hex Girls appear in the woods, and right behind them is the witch. Scared by the creepy creature, the three of them run for their lives. The witch tries to grab them, but is captured by Daphne and Fred.
The witch is revealed to be McKnight, Thorn's father. Velma then explains that the truck they saw in the barnyard was being used to lift the witch and made her appear to fly, and that the fire balls are actually fireworks. She also deduces that many townspeople were in on the trick, including Jack and the Mayor. Back at Ben's house, the writer scolds the people involved for exploiting Sarah's good name for their benefit, and the gang apologizes to the Hex Girls, for thinking that they were real witches. Thorn and the girls decide to explain that the ritual Fred and Daphne saw was just to improve her vocals, and that she is actually 1/16th Wiccan. The Mayor and McKnight explain that they had to use the witch to boost the town's economy because of the lack of tourists. Also, the Mayor recalls that Ben once told him that supernatural phenomena always attracts people. Trying sooth things a little, the Mayor and McKnight tell Ben that they did find the head marker for Sarah's grave, while digging for artifacts where the Puritan village is located, but they still do not know where the grave is located. According to them, Sarah's grave could be anywhere from Miller's Creek to the Old Tree Stump. Hearing that, Velma then remembers about the buckle Scooby found, and that he found it while digging near the Old Tree Stump. She goes to where Sarah's portrait is, and finds out that the buckle is the same one in Sarah's diary. They all quickly realize that her grave must be located near that tree stump.
The gang, Ben, the Hex Girls, McKnight, and the Mayor go to the spot where Scooby found the buckle. Velma then asks Scooby to dig deeper, to see if they canfind anything. After initially refusing, Velma convinces Scooby, by giving him two Scooby Snacks. The Great Dane digs deeper and after a short time, he discovers a chest. When Ben opens it, what they find inside is not a diary, but a spell book… A witch's spell book. It is then that Ben explains to all of them that he knew from the beggining that Sarah was indeed a witch, and that the Wiccans had trapped her inside her own spell book. For years he had tried to find that spell book, but he never found it. When he read about the gang's accomplishments, he divised a plan in order to meet them. He paid the archeologists and the security guards, so they would stage the whole thing in the museum. That way, he would be sure that he would end up meeting them. Ben knew that if there was someone who could find the book for him, that would be Scooby and the gang. He also says that if he had tell them the truth, they would have never helped him in the first place. Velma then accuses Mayor and McKnight of knowing about Ben's plan and that they helped him, but the writer states that the witch's trick was the town's idea, and that they weren't in the secret.
Becoming insane with his new magical powers derived from the book, Ben quickly captures McKnight, the Mayor, and the Hex Girls before trying to get Sarah out of the book. Scooby and the gang try to stop him, by grabbing the book. And although they are able to grab the book, they loose it again, and in the process, the only thing they are able to do is to completely wreck the Mystery Machine in a wild pursuit. After being sure that the Mystery Inc. will not cause him anymore troubles, Ben is able to get Sarah from her prison. He then tells her that he wishes to rule the world by her side, and for her to teach him everything she knows, but Sarah's ghost rejects Ben's idea of ruling the world together, and instead wishes to destroy it. Horrified by this, Ben attempts to imprison Sarah back in the book, but she says only a true Wiccan can return her to her prison. She then casts an energy sphere around Ben, and begins to create na army of mosters to help her in her vendetta.
Velma then has a brilliant idea. She frees the Hex Girls, and while Dusk and Luna try to release the Mayor and Mr. McKinght, Velma convinces Thorn to read the spell. Initially, she refuses, but then understands that she's the only one who can stop Sarah. Velma then sends Scooby and Shaggy to get the book, while the rest of the gang distracts Sarah, who keeps turning pumpkins, trees, and even a turkey into monsters to stop them. Eventually, the gang obtains the book, each throwing it to another person when they get captured, until it reaches Thorn. Thorn reads the spell, sending the witch back to the book from where she was realeased.
But Sarah decides that she will not go back to the book alone, and grabs hold of Bem, who had been previously released from the energy sphere where he was trapped, at the last second, and they get both sucked into the book. A burning branch falls on the book, disintegrating it (apparently forever trapping or killing the two villains). The gang then frees the others, and the witch's monsters turn back to normal, with the exception of the giant turkey, who becomes the town's newest attraction. In order to repair the damage caused in the fight, the Hex Girls and the gang give a concert to the townspeople and the tourists performing the song "Earth, Wind, Fire and Air".