Leatherhead heads to New York to get revenge on the Teenage Mutant Ninja Turtles. He runs into the Rat King instead, who has stolen a truckload of chemicals and plans to turn the citizens of New York into mindless zombies so his minions of rats can rule the city. With two of their most insidious foes in the same sewer, the Ninja Turles must work with April O'Neal to stop them both.

The Turtles must clear their names when they are believed to be jewel thieves who stole a priceless emerald during a magic act run by a wizard named Boldini.