The main gameplay loosely adapts the following season one episodes: "Things Change", "A Better Mouse Trap", "Attack of the Mouser"s, "Meet Casey Jones", "Nano", "Darkness on the Edge of Town", "The Way of Invisibility", "Notes From the Underground" (Parts 1-3), and "Return to New York" (Parts 1-3), as well as a level that is not derived from the animated series at all.