Dinosaurs invade the Big Apple. Befriending a young diplodocus the Turtles trace the invading dinosaurs to their source finding a lost world.

In an attempt to hijack two separate trains carrying the ingredients needed to make mutagen, Rocksteady and Bebop cause their head-on collision, resulting in the spillage of both chemicals in the city's train yard.

In an effort to rid himself of the Turtles, Shredder with the help of Rocksteady and Bebop kidnap Obento, caretaker of the Far East Animal Society then blackmail Usagi Yojimbo into destroying the Turtles.

While the Turtles are suffering from turtle pox, a disease that affects only mutant Turtles, Krang has developed a robotic turtle that he calls Metalhead.