Abandoned by his mother shortly after immigrating to America, Gon is raised by the mafia and grows up to become a cold-blooded hitman. While on a job, Gon makes the mistake of killing an innocent young girl. A flood of guilt takes over his life and the situation becomes worse when his boss assigns him the job of killing the young girl's mother. The trouble is, he falls in love with her.

After super villain Shredder escapes custody, he joins forces with mad scientist Baxter Stockman and two dimwitted henchmen, Bebop and Rocksteady, to unleash a diabolical plan to take over the world. As the Turtles prepare to take on Shredder and his new crew, they find themselves facing an even greater evil with similar intentions: the notorious Krang.