After the defeat of their old arch nemesis, The Shredder, the Turtles have grown apart as a family. Struggling to keep them together, their rat sensei, Splinter, becomes worried when strange things begin to brew in New York City.

When Scooby and the gang get trapped in a video game created for them, they must fight against the ‘Phantom Virus.’ To escape the game they must go level by level and defeat the game once and for all.