Mook Animation is an animation studio based in Japan and started in 1986. Mook Animation formed a business alliance with DLE in 2006 and was known as Mook DLE; however they ended their partnership in 2008. Mook has created Animation for Western programs, mostly for Hanna-Barbera and later Cartoon Network, such as SWAT Kats (four episodes from the first season and the entire second season), The Real Adventures of Jonny Quest, Scooby Doo on Zombie Island, Scooby-Doo and the Witch's Ghost, Scooby-Doo and the Alien Invaders, and Scooby-Doo and the Cyber Chase. They provided the Animation for Transformers: Animated which debuted spring 2008 on Cartoon Network.
After Ben Ravencroft, a famous horror writer of whom Velma is a big fan, assists her and the Mystery, Inc. gang in solving a case at a museum, he invites them to his hometown, Oakhaven, Massachusetts. When they arrive, they find the town converted into a tourist attraction by Mayor Corey, complete with 17th-century replicas and attractions based on the alleged ghost of Sarah Ravencroft, an ancestor of Ben's who was persecuted as a witch and executed by the Puritan townspeople in 1657. Ben disputes this, claiming Sarah to be a Wiccan who used natural herbs to heal people and reveals for years he has been searching for Sarah's medical journal to prove her innocence.
In a college computer lab run by Professor Robert Kaufman, as he goes to check on his two students; Eric Staufer and Bill McLemore, a new creature - the Phantom Virus - comes out of a new game based on the Mystery Gang's past adventures and tries to scare away the game's creator Eric. The next day, Mystery, Inc. themselves come to the college and learn from their friend Eric, that the virus had assumed a lifelike form thanks to an experimental laser which is able to transmit objects into cyberspace, and is now rampant across the campus. The gang goes on the hunt for the Phantom Virus, where the virus chases Scooby and Shaggy through the college. Unfortunately, the whole gang, including the virus, somehow gets pulled into the game after 'someone' activates the laser. Left with no other choice, the gang fight their way through the ten levels of mystery and adventures to complete the game in order to escape it, with the goal of finding a box of Scooby Snax to complete each level. Their efforts are impeded on each level by the Phantom Virus. The first level is on the moon, the second is in the Roman Colosseum, the third is in the dinosaur age, the fourth is under the sea, the fifth is in a (shrunken) backyard, the sixth is ancient Japan, the seventh is in ancient Egypt, the eighth is in medieval times, and the ninth is in the North Pole.
The Mystery Machine is driving through the Sonoran Desert. A sandstorm comes up and Shaggy Rogers makes a wrong turn onto government property. Seeing a UFO causes Shaggy to lose control of the vehicle and the gang find themselves on the outskirts of a small town. While Scooby-Doo and Shaggy stay with the van the rest of the gang enters a local diner to get directions. Shaggy and Scooby then see a mythical animal called a jackalope. The jackalope takes their last Scooby Snack and they chase it into a cave, where they encounter aliens. They run into the diner in panic, claiming to have seen aliens.
The movie opens with Mystery, Inc. being pursued by a moat monster. After an accident with Scooby-Doo (Scott Innes), he is caught and revealed to be a counterfeiter. This is actually an old case of the now-dissolved Mystery, Inc., who went their separate ways because they were frustrated with their mysteries having all involved mere crooks in monster costumes, as told on a talk show program by Daphne Blake (Mary Kay Bergman), who now, along with Fred Jones (Frank Welker), is running a successful TV series Coast to Coast with Daphne Blake, which involves her and Fred going to historic and inspiring places all across the country. For the show's upcoming second season, Daphne intends to visit haunted and mysterious places and track down real ghosts. When Daphne confesses on air that she misses the gang and that she wishes they were with her, Fred arranges a reunion and contacts Velma Dinkley (B.J. Ward), who has gone on and become the proprietor of a mystery bookstore, and Scooby and his owner Shaggy Rogers (Billy West), who have been bouncing from job to job, including working in customs at an airport, from which they were just fired after eating all the confiscated imported foods. The reunited gang surprise Daphne on her birthday and they go for a trip to Louisiana for her show.