A strange virus from a new game based on the gang's past adventures comes to life and tries to scare away the game's creator, so Mystery, Inc. themselves come to help their friend. They come to the college where the game was created and learn from their friend and the creator Eric, that the virus has assumed a life-like form and is now rampant across the campus. The gang goes on the hunt for the mysterious computer virus. Unfortunately, they somehow get pulled into the game after a mysterious villain activates the game in cyberspace. Left with no other choice but to complete the game in order to escape it, the gang fights their way through ten levels of mystery and adventure, with the goal of finding a box of Scooby Snacks in order to complete each level.