April O'Neil, an ace reporter for Channel 6, investigates recent break-ins, allegedly by Ninjas, which have resulted in the thefts of numerous technologies.

April and the Turtles embark on a mission to save her dad, but they eventually have to confront Shredder himself, who's taken the job of destroying the Turtles into his own hands.

Baxter Stockman, a mad scientist, has created new invention: a rat catching robot called Mouser. Shredder mass produces the robot and programs them to hunt the biggest rat in New York – Splinter. A dozen Mousers are released in the sewers. Meanwhile, Michaelangelo finds out about Krang, who tells him to destroy the master control for the Mousers.

In the Technodrome deep under New York City, Krang reminds The Shredder that once again he has failed to destroy the Turtles. Krang demands a "body", mentioning his old home, Dimension X - which gives Shredder the idea to open the recently completed "Transdimensional Portal" so that he can retrieve advanced weapons to use against the Turtles. However, when Shredder opens the portal, he lets out three teenage Neutrinos in flying cars, chased by a flying jeep piloted by two of Krang's Stone Warriors. The Neutrinos blast through the Technodrome and escape. Bebop and Rocksteady fire on the Stone Warriors, General Tragg and Lieutenant Granitor, until Shredder establishes that they work for Krang.

Shredder creates a Retro-Mutagen Ray Generator that can reverse any mutation and dares the Turtles to come get it. As Donatello tries to create a fuel source for the vehicle that The Neutrinos left behind, Splinter and the Turtles eventually make their way to the Technodrome just in time to discover Krang in his new body.

Shredder returns from Dimension X and sets out to frame the turtles with a group of thugs dressed as them while Dr. Baxter Stockman uses the Ultimate Rat Catcher on Master Splinter.