Shortly after a group of Mouser Robots destroy the Turtles' old home, they begin to attack their new home. Eventually the Turtles trace the robots back to Baxter Stockman's factory, where they save young April O'Neil. Afterwards Michelangelo gets on Raphael's nerves, making Raphael leave to the surface. At the surface, he is confronted by Purple Dragons' thugs, and meets Casey Jones, who equally hates that gang. Afterwards Stockman develops for the Foot Clan invisible Foot Tech Ninjas to capture Raphael, forcing the Turtles to rescue them and Donatello to use a cloaking device detector to properly fight the invisible ninjas. Afterward, they are confronted by genetically mutated beings. Once all four levels are completed, the Turtles strike on the Foot Headquarters, where they fight Hun before going after the Foot leader, The Shredder.