After a fight with Shredder causes Donatello to be struck by a laser beam, his personality changes to become a costumed superhero known as the Dark Turtle. His mission: Seek out & destroy Shredder. Meanwhile, a dinosaur-like alien race called Triceratons, invades Earth.

While Splinter's sensei, Mogo-san, is visiting New York, a criminal gang of ninja, known as the Black Heart Gang, are terrorising the city with a crime spree, and Mogo-san's grandson, Yoku, is their leader.