The turtles find out where the Ooze, the substance which made them mutate, came from. Unfortunately the Shredder returns and learns about the ooze too, and uses it to enhance himself. So now the turtles have to prove again who's the better ninja fighters and save the city from a new Super Shredder & his new mutants, Tokka & Rahzar.
April O'Neil: I guess you're not the ones that can handle this.
Chief Sterns: That's what we do best, Miss O'Neil.