Tired of fixing everything in the lair, Donatello decides to clone himself so he can work on his other inventions. However, Donatello's clone turns against him and joins the Rat King in an attempt to conquer the city with a rat infestation.

While on a visit to an Egyptian Exhibit, Michelangelo is mistaken for a Pharaoh named "Amun Turt-El", also known as "The Sacred Turtle".

Frip the Polarisoid arrives back on Earth with his family for a visit, and must ultimately ask the Turtles for help in reclaiming his camera while helping them stop Krang's latest plan to conquer the city.

Zach, the Turtles' young friend, is put into military camp by his parents after making numerous false reports of aliens, only to find two real aliens--Wingnut and Screwloose--brainwashing the cadets to be their army and must call in the Turtles to defeat them.

A mad professor named Mindbender creates a law-enforcement robot named "LEX" to clean up crime in New York, but LEX ultimately starts arresting numerous innocent people for the smallest infraction. With the other Turtles unreachable, Leonardo must discover his own innate skills to stop this rogue robot before he and Mindbender declare themselves dictators of the city.

Raphael's latest study of disguises leads the Turtles to attempt a rescue when he is mistaken for a mobster named "Mad Dog McMutt".

Using a hypnotic microphone and speaker, Shredder takes over a radio station and broadcasts a signal that sends the population of New York City sailing into a dimensional limbo dubbed "Krang's Chasm".

A nerd-turned-muscleman captures three of the Turtles, and a reluctant Leonardo must ask Casey Jones for help in rescuing them.

Bebop and Rocksteady botch another mutagen experiment, resulting in a giant ice creature who Bebop dubs "Frosty", and Shredder uses this monster to freeze New York solid, preoccupying the Turtles long enough for him to steal thermal explosives needed to melt the Technodrome free from the ice.

Baxter Stockman leads a swarm of flies in an attempt to conquer New York and prove his worth to Shredder and Krang so he can become human again.

A malfunction of Donatello's latest invention ultimately results in Raphael believing he is about to die, and ultimately trying to save the world by himself.

While testing an experimental Muta-Shooter invented by Krang, Shredder unexpectedly turns Napoleon Bonafrog into a muscular, monstrous version of himself.

An accident causes two garbagemen to mutate into Muckman and Joe Eyeball. Muckman's slime is found to weaken the Turtles, and Shredder tricks him into working with him.

When the city is hit with a sudden termite infestation, the only superhero who can help - Bugman - is too at peace with himself to aid the Turtles in defeating it.

Donatello has tricked out the Turtle Van, but while taking it for a test drive, it's stolen from him by a family of robbing hillbillies. Can Donatello get the Van back in time before his brothers find out?

A delivery boy accidentally falls into Krang's new unstable Mutagen and becomes able to transform into anyone he chooses. Shredder tricks him into helping him launch the Mutagen into space and mutate the world, but this "Mutagen Man" has other ideas.

Michelangelo's strange dreams lead him to seek out Mondo Gecko, a lizard who was caught in the same ooze as the Turtles. Gecko eventually rebels against his boss, Mr. X, and his bombing campaign.

Set up as a follow-up episode, Hokum Hare and the Turtles hitch a ride on a time-traveling train to 2036, where they discover that Shredder has plans for the future New York City. Ultimately, the Turtles of both the past and the future must team up to thwart Shredder before his actions cause all of time to be destroyed.

The Turtles travel to a FairyTale Dimension in an attempt to save the city from Shredder's Docilizer, while also making friends with a local citizen of that dimension, Hokum Hare.

A family secret is revealed when Lieutenant Kazou Saki arrives from Japan to arrest his brother Oroku Saki, who turns out to be the Turtles' greatest enemy. Shredder and Krang send the Technodrome from Dimension X to Earth, but Donatello re-programs it to crash in the Arctic.

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.

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.