The Ninja Turtles comes into conflict with T.C.R.I. scientist Dr. Baxter Stockman with the association of the Foot Clan and the return of the Shredder, who has hired Stockman to create mutants of their own in the form of Bebop and Rocksteady and an unknown invasion above New York City. To prevent the end of the world, the turtles and their human friends April O'Neil and Vern Fenwick comes to the aid with vigilante Casey Jones.