Mystery Inc. visits their old friend and college student, Eric, who has invited them to see a prize-winning computer game he made based on their adventures and a high-tech laser, both of which he intends to enter at a campus science fair.

Upon arrival, the gang learn a "Phantom Virus" materialized from Eric's game and attacked him before his teacher, Professor Kaufman, drove it off with a high-powered magnet and that it has been terrorizing the campus ever since.

After escaping from the Phantom Virus, the cyber-gang reveal that they know where to locate the final box of Scooby Snax and lead the original gang to an amusement park, where they battle real versions of monsters that Mystery Inc. have previously faced and unmasked as human criminals.

Arrested by Wembley, Bill reveals that he was jealous that Eric's video game was chosen for the science fair over his even though he had been at the school two years longer, so he created the Phantom Virus to scare Eric away and claim the prize money for himself; fearing that Mystery Inc. would discover he had created the virus, he beamed them into cyberspace in the hope that they would not survive.

For Cyber Chase, it was the same situation: executives recommended Mark Turosz, a writer already under contract with Warner Bros. who had little experience with animation.

The crew had produced the first Scooby film, Zombie Island, as well as the third, Alien Invaders, with total autonomy, and were insulted by Warner's insistence that they use Turosz's script.

[2] Stenstrum initially suggested they explore using live-action actors for scenes set inside the video game, though the idea was quickly dropped.

Out of the first four films, Cyber Chase features the largest array of storyboard artist credits, as the team were under significant time constraints and required additional help.

[4] Common Sense Media gave the film a two out of five stars, saying, "Fine for fans of the franchise, but too much cartoon jeopardy for little kids.