The Phantom Virus (voiced by Gary Sturgis) is the main antagonist of Jeffrey, Jaden & Friends' Storm Adventures of Scooby Doo and the Cyber Chase. The Phantom Virus was created to try and sabotage a fellow college student's project to win a large amount of money. It can steal computer data, and has a weakness to magnets. When the gang was sent inside the computer game, the Phantom Virus tried to destroy them in each level. But he was finally defeated when they won the game.
- The Phantom Virus will return in Jesse, Xion & Luigi's Mansion: Dark Moon.
- The fact the virus is scared of/hurt by magnets may be a reference to how magnets harm computers.