Shredder breaks into the Ninja Hall of Fame and steals the diary of the famous Brothers Kojima. He leaves his fingerprints all over the place though, and one Lieutenant Saki, Shredder's brother, finds them.

Michaelangelo awakes in the middle of the night from a bad dream. Unable to remember what it was about, Splinter assists him through hypnotism. Mikey vividly recalls the day that he and his brothers fell into the sewer and landed in the green ooze but he also sees a small lizard crawling through the contaminant.

In the frozen tundra of the Arctic Polar Cap, Krang rants and raves that Rocksteady and Bebop will not return in time with the Bindex 3 to load the mutagen into the rocket ship's fuel tanks before lift off. Krang' plans turn all the City's inhabitants into horribly disfigured mutants from the vapor trails of the fuel used to lift the rocket.

While road testing the Turtle Van with his latest inventions, Donatello encounters a family of criminal hillbillies known as the Badd Family.

Michaelangelo and the other Turtles go topside in an effort to find the latest issue of "The Adventures of Bugman", only to learn that the comic book has been canceled.

Attempting to de-mutate the Turtles, Krang sends Shredder, Rocksteady and Bebop to the Earth's surface to retrieve Compound X-7.

While Krang hires some local hoods to drill for anti-freeze Shredder, Rocksteady and Bebop visit the Louisiana Swamps in search of the Mutagen Pool.

Thanks to a malfunction in Donatello's Healthometer, an invention designed to diagnose one's health, Raphael is convinced that he is not long for this world. Raphael decides to make the world a better place with what little time he has left.

Baxter Fly is back, and this time he has assembled an army of flies to infest the city, endangering millions just so Stockman can get to Shredder.

Donatello decides to create a clone of himself so that he can spend more time on his inventions while his clone spends more time fixing things around the Lair. Donny tests his latest invention on a sewer rat and accidentally gets his hand in the way, causing the rat clone to talk just like Donatello.

While the Turtles do battle with a refrigerator that has not been defrosted lately, Rocksteady and Bebop decide that they want to be the top mutants at the Technodrome and throw out a vat of mutagen onto the frozen tundra, creating a giant Ice Creature.

A series of baffling crimes are being committed by "brawny burglars" with thick Austrian accents and the Turtles are on the case, but so is Casey Jones and that could mean nothing but trouble for the Turtles.

The turtles, Groundchuck and Dirtbag are taken to Shellri-La by an alien "Turtleoid" named Kerma. Kerma seeks help from the turtles to defend his planet from a two-headed dragon named Herman the Horrible.

The turtles unmask the dragon as they prove that the menacing creature is actually operated by two renegade Turtleoid delegates. Kerma return the turtles back to Earth, where they destroy Shredder's new Technodrome Mark II and afterwards defeat Chrome Dome.

Krang's attempt to split the Inter-Dimensional portal goes awry. By utilizing the pirate radio station WOOF Krang believes that he can use the station to lure the City's populace into Krang's Chasm.

Raphael's ego is bruised when the other Turtles laugh at him for taking a correspondence class in the art of disguise. Raphael challenges his brothers to go to Central Park and pick him out of a crowd.

The City Mayor announces an end to crime when he introduces Professor Mindbender and the professor's latest invention: LEX, a robotic police officer. LEX rids the streets of crime enough to allow the Turtles to take a vacation.

Zach, the Turtles' young friend, and honorary fifth Turtle, is infatuated with comic books, especially 'The Alien Invaders.' Zach retires his Turtle costume when his parents enroll him in the Ten-Hut Military Academy where they hope he will learn some discipline and live in the real world.

Krang wants to get a hold of the Polarisoids' camera. Krang sends a fake invitation to the Polarisoids to visit Earth, only the Polarisoids think that the invitation is from the Turtles.

While the other Turtles go off to the local Planetarium to see O'Malley's comet, Michaelangelo visits the Natural History Museum with April O'Neil for the unveiling of the mummy of Ahmed Turt-el.