The Mystery Inc. gang meets with their friend, Eric Staufer, a computer science major at the university, who created a laser that can send people into cyberspace. A video game featuring Scooby and the gang was designed to test the laser, but during the test, a Phantom Virus has escaped from cyberspace, causing chaos in the university. Can Mystery Inc. stop the Phantom Virus and find out who is responsible for releasing it?
In Scooby-Doo and the Cyber Chase for Gameboy Advance, you must discover the identity of the suspect responsible for unleashing the Phantom Virus by navigating seven levels. Each member of the Mystery Inc. gang can be used, but only one character can play at a time. You'll need to collect CDs to unlock access to additional levels. The game also features pick-ups such as disguises, smiley faces, Scooby Snacks, and a Scooby Snacks Box that will help you progress through the game.
Each level consists of various challenges, including fighting monsters and villains, with some containing classic Scooby-Doo characters or the Phantom Virus. Defeating the villains will allow you to complete the level, while avoiding the Phantom Virus's electric bolts is crucial until you collect enough Scooby Snacks to progress. If your character's health is reduced, they'll be captured in cyberspace, and another character will have to try the level.
Points are earned for collecting Scooby Snacks and evading monsters, while clues can be collected throughout the game. The game saves via a password system, recording your progress and score after each level. After finishing the final level, you'll be asked to identify the suspect responsible for unleashing the Phantom Virus based on the clues you've collected.