Plot
The movie opens with a flashback of a young Vincent Van Ghoul and his partner, Mortifer Quinch successfully hunting down and sealing the 13th Ghost in the Chest of Demons. However, Mortifer was attacked and seemingly killed by minion ghosts as a tearful Van Ghoul makes his escape. In the opening credits of the movie, Van Ghoul recaps the events of The 13 Ghosts of Scooby-Doo in which Scooby-Doo set the 13 Ghosts free once more by accident, but would catch all but one with the help of Shaggy Rogers, Daphne Blake and young Flim-Flam.
In the present day, Scooby, Shaggy, Daphne, Fred Jones and Velma Dinkley chased Farmer Morgan through the shopping mall and eventually captured him in Old Timey Toys. When the gang tried to unmask him, Morgan appears to be the real deal. Just then, the sheriff arrives with the real culprit, Mrs. Malveaux who stopped a deal with Morgan. The sheriff chastises the gang for capturing the wrong suspect, and he threatens them that if he ever sees them driving around in the Mystery Machine, he will put them in jail and also reminds them of the new leash law for dogs. With that, he tells the gang to stop solving mysteries.
The next day, the gang had a garage sale, selling all the monster costumes from their previous mysteries, as well as the Mystery Machine, much to Fred's misery. While Shaggy and Scooby relax in deckchairs, a customer named Bernie Alan discovers the crystal ball amongst their old mystery stuff, making Shaggy and Scooby recognize it from their 13 Ghosts adventures. Just then, Van Ghoul contacts Daphne, Shaggy and Scooby about the 13th and final Ghost. When Fred and Velma enquire what is going on, Daphne fills them in on her 13 Ghosts mysteries with Shaggy and Scooby while Fred and Velma were away from the gang after the events of Scooby-Doo and Scrappy-Doo.
After changing into her old 13 Ghosts outfit, Daphne unveils her old red van, the Miss-tery Machine to Fred and Velma, and the gang start on their journey to meet Van Ghoul at his castle. On their way, the gang were chased by a phantom car, but Daphne managed to outmaneuver it skillfully. When Fred saw Daphne took charge, it furthers Fred's existential crisis as he feels he is without a role. When the gang meet Van Ghoul, they were attacked by the 13th Ghost; a winged demon named Asmodeus. Shaggy sheepishly reveals that he sent the chest to Van Ghoul's residence in the Himalayas, and the gang heads over there using a flying boat.
When they arrived, the gang encounters Bernie Alan who inquired about the crystal ball at their garage sale, and Daphne, Shaggy, Scooby and Van Ghoul trailed him, but then get attacked by the phantom car and it revs its engine to cause an avalanche. Van Ghoul reveals that he is unable to use his magic powers and the four crash into a temple. Meanwhile, Fred and Velma search a seemingly abandoned post-office in a village, and they meet Flim Flam now an adult and he tries to sell them his Chest of Demons merchandise and ghost-catching equipment. When Fred and Velma leave the shop, they were suddenly snatched up by something even Velma cannot explain.
At the temple, Asmodeus had been waiting for Van Ghoul and he chases the four when they find the chest. While running, Van Ghoul destroys his crystal ball and transports Shaggy, Scooby and Daphne outside the temple where they meet Fred and Velma. As the gang fell into despondence, Fred reveals that he actually went to a cheerleading school during his time away from his friends. As Fred cheers for his despondent gang, a restored Daphne concocts a plan.
Velma visits Flim Flam's store and takes everything. Suddenly, the phantom car pursues Fred, Velma and Flim Flam, but they evade with the Miss-tery Machine's installed upgrades. Meanwhile, Shaggy, Scooby and Daphne infiltrate the castle to rescue Van Ghoul, and they reunite with Fred and Velma and Flim Flam who asked about Scrappy, which confuses the gang for a moment. Going into the castle, they find Van Ghoul defeated. He reveals to the gang that Asmodeus is really the demon form of his magically powerful ancestor, Asamad Van Ghoul and blames the impending doom on himself.
Asmodeus opens the Chest, something Velma points out as being possible, as the Chest can be only opened by a living person. Asmodeus tries to escape, but he gets intercepted Daphne. Asmodeus was unmasked as Mortifer, who reveals that he faked his own death by casting an illusion to fool Van Ghoul and he explains that he wanted to sell Flim Flam the Chest for $10 million. Bernie Alan arrives, and he reveals himself to be an Interpol agent named Vance Linklater and he arrests Mortifer. Just as Mortifer was taken into custody, he escapes in the phantom car but gets recaptured.
A visage of the real Asmodeus and Asamad briefly appears before the gang, and Velma deduces a tome that the real Asmodeus was really watching over Van Ghoul, and he has achieved redemption. She however fabricated the story to give Van Ghoul closure and debunks that the 12 Ghosts as hallucinations due to the Himalayan thin air and teases opening the real Chest, but after seeing everyone's fearful faces, she decides not to.
As the gang get ready to depart for home, Daphne kisses Flim Flam as a thank you for his help, and Van Ghoul warns Flim Flam to stay out of trouble. As they fly back home, Daphne decides the gang should continue solving mysteries and gives the leadership job back to Fred.
