[7] "Those meddling kids" and their Mystery Machine are at the center of a well-meaning experiment gone wrong and they will need to bring all of their mystery solving skills to bear (along with plenty of Scooby Snacks) to find a cure for a world full of mutated creatures infected by a nanite virus that enhances their fears, terrors, and baser instincts.

Scooby-Doo, a subject prototype in the Complex's Smart Dog program, and Norville "Shaggy" Rogers, his trainer, are attending the Blazing Man Festival nearby, when Scooby is alerted to Velma's attack.

Shaggy remembers one scientist was working on an armored van designed for an apocalypse-like scenario, dubbed the Mystery Machine, which the group uses to flee the Complex.

While driving away from the Complex, Scooby and Shaggy notice the Blazing Man festival has been completely overrun with Beasties, meaning that the nanite plague was not just contained in one area, as hoped by Velma.

The group is able to get Fred's leg fixed up, while Velma is able to get a laptop to hack into the Complex's network and access its files.

When Velma had released the final set of nanites in Paris, she discovered the truth about the Four going behind her back and changing the goals of Project Elysium, and decided to contact Daphne in the hopes of releasing her story, as her brothers' influence would be able to detect and shut down the story if it was coming from the mainstream media.

In order for the pack to survive, they need to keep the human intellect they have gained, which means they need to find Velma to fix their implants.

Scrappy realizes that he needs to become stronger if he and his pack want to live, so he activates some experimental nanotechnology embedded in his body, dramatically increasing his size and strength, and allowing him to walk on only his hind legs.

While Scrappy and his pack track Velma, he finds a boy named Cliffy, who lost an arm and his family to the Beasties.

Velma believes that due to the nanites, the Beasties are working as a hive mind, and are migrating to some location.

As they get closer, they notice that several cars on the road to Seattle have been abandoned, making it nearly impossible to drive there.

Fred, still with an injured leg, is forced to stay in the Mystery Machine, while the rest head to Dinkley tower.

While Velma confronts her brother, Fred calls Shaggy, as he notices the Beasties have built a giant statue shaped like Rufus, and are climbing up the Tower.

As the group move through Washington, Scooby tells Velma that he can hear a signal that's directing the Beasties to some location.

However, Scrappy, Velma, Scooby Doo, and Cliffy encounter a group of Beasties, who attempt to attack them.

Scrappy finds out that the Beasties are coming together to form one giant being, controlled by a Beast with a rather intelligent mind.

Sometime around Christmas Eve in Wisconsin, the group head to a place known as the Athena Center, which housed the Complex's cloud servers and backup data.

When they look outside the room, they find that the matured Beasties are all dead, likely due to a psychic link between the children and the parents.

Six months later, the Hudson Mall has been turned into Jonestown, a shelter for the humans who survived the nanite plague, named after Fred.

While some citizens of Jonestown rescue a few survivors, they find Fred, who appears to be in a zombified state, approaching them.

Surprisingly, the electric shock fixes Scooby's implants, causing him to speak with a fully intellectual mind, rather than his usual limited vocabulary.

At Jonestown, Cliffy tries to cope with Scooby's new intelligence, as he feels that he will lose him, just as he has lost his friends and family in the apocalypse.

While Shaggy is ecstatic, the celebration is cut short when Scrappy comes back and tells them that Zombie Fred has kidnapped Daphne.

As the gang approaches, a helicopter arrives, carrying Velma's brothers, Quentin and a severely burned Rufus.

Rufus, like most inhabitants of Jonestown, had a biological immunity to the nanites, but while the vaccine helped prevent dying from the fire, it was destroying him, making him mentally unstable, as Daisy and the others had seen when they last saw him in Seattle.

Daphne, Velma, Shaggy, Scooby, Daisy, Cliffy, Scrappy, Quentin, and Rufus all manage to survive by hiding in the sewers, along with a handful of Jonestown citizens.

An excited Velma states that with the technological advancements that surpass the Nevada Complex, and with the information of the experimental vaccine Quentin used on Rufus, she can make a cure.

The story ends with Velma giving birth to a baby boy: Frederick Rufus Rogers-Dinkley.

Shaggy and Velma name Daphne (now living with a still-alive Scrappy) as Frederick's godmother and Scooby-Doo as his godfather.

works with Agent Honey Bea of MI6, an ex-girlfriend of his, as well as Morocco Mole (who is now the Chief of the I.S.S., although Secret Squirrel himself does not acknowledge this) to discover who has been killing scientists all over the world and stealing their brains.