The Turtles learn the cost of slacking off when Splinter is badly hurt during a confrontation with Shredder.

The intentions of the Turtles are put to the test when a controversial TV-figure portrays our heroes as menaces to society. The Turtles forego publicly clearing their name to defeat Krang and his new robotic weapon.

• First appearance of Krang's "bubble walker"

Irma accidentally becomes gigantic and her naturally clumsy nature makes her a danger to the city. The Turtles and April O'Neil hide her and search for her cure.

Title Reference: Attack of the 50 Foot Woman.

Gangsters are swiping all the antiques in town. And when they swipe most of our heroes, it's up to Donatello and April to find out why. Could Shredder be behind this?

Title Reference: The Maltese Falcon

• In this episode, Burne Thompson is voiced by Townsend Coleman instead of Pat Fraley.

The Turtles go flying when the Shredder invents a gravity-altering device. Soon it extends to the surface and affects all of New York City.

The bodies of Shredder and Splinter are switched when a device is accidentally activated during a battle between the Turtles and their enemies. As Shredder plans the Turtles' demise and Splinter plans on how to get back to his body, everyone else is clueless

In the middle of a summer heat wave, someone is destroying all the air conditioners and taking all the city's freon. In the meantime, Vernon and Burne go looking for the Turtles, but find something else.

• First appearance of Don Turtelli

A 13-year-old boy tries his best to help out the Turtles, but with some not so optimal results. In the end, he proves himself to be a great asset to the Turtle team.

• First appearance of Zach and his brother Walt.

A mysterious, sewer-dwelling man has an unnatural ability to put rats under his control. Can Splinter resist, or will he destroy the Turtles at the bidding of the Rat King?

Notes: This is the very first episode not to feature Shredder. First appearance of the Rat King. In this episode, Burne Thompson is voiced by Townsend Coleman instead of Pat Fraley.

After witnessing a living dinosaur wander in the city and disappear abruptly, the Turtles follow its tracks into a large hole, where they discover a shocking revelation: A cave where dinosaurs still roam. Meanwhile, Shredder and his mutant goons, Bebop and Rocksteady, are also there, but to collect a crystal needed by Krang to recharge the power cells of the Technodrome. The Turtles discover that the crystal is the source for all lifeforms inside the cave, and must get it back before they are all destroyed.

Title Reference: Tarzan at the Earth's Core

Emperor Aleister of Malicuria comes to the United States with a sample of Lydium 90, which gets noticed by Krang as a way to power up the Technodrome, which has constant brownouts. To celebrate relations between Malicuria and the US, the Emperor hosts a masquerade ball in New York, but his bored daughter and April's exact double, Princess Mallory sneaks out for a night on the town. April crashes the party dressed as a princess, and gets mistaken for Mallory, but the masquerade is also crashed by Shredder, Bebop and Rocksteady, who plans to kidnap Mallory in order to get the Lydium 90 shard.

• This episode is inspired by Mark Twain's The Prince and the Pauper.

A robot warrior, known as the Mobile Armored Computerized Combatant (M.A.C.C.), arrives from 400 years in the future in 20th-Century New York. He befriends the Turtles, but Shredder and Krang are looking to bring him to their side, at any means necessary.

• Ace Duck is briefly seen on the Turtles' television, making his only appearance in the series.

Shredder gains possession of an ancient ninja sword that is crafted from an alien metal, allowing it to 'cut' through dimensions.

• In this episode, Raphael is voiced by Thom Pinto instead of Rob Paulsen.

Krang and Shredder's plan to flush out the Turtles from the sewers leaves the city flooded with water (and creatures!) from the Atlantic Ocean.

Title Reference: Twenty Thousand Leagues Under the Seas

Notes: Final Appearance of Tiffany. In this episode, both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon.

Worried that Shredder will soon win, Leonardo takes some time off, doubting his leadership. Meanwhile, Krang and Shredder drain solar energy from the Sun for the dual purpose of powering the Technodrome and capitulating Earth into another Ice Age. Without Leonardo, the three other Turtles try to thwart Shredder while taking turns as leader, but each realizes they need to overcome their own flaws, such as Raphael sticking to a decision, Michaelangelo becoming more serious and Donatello needing to analyze even the most obvious facts.

Title reference: Take Me to Your Leader

A bump on the head leaves Leonardo thinking that he is in 17th century France, and that he and his comrades are Musketeers.

Title Reference: The Three Musketeers

Notes: In this episode, both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon. This episode was part of the TV Teddy video range where the titular teddy bear interacted with scenes and the presenter of the video.

Shredder programs the city's new garbage collecting super-computer to collect the Turtles. But when Shredder doesn't specify 'Ninja' Turtles, the super-computer collects them all! Turtles of the city of every shape and size are not safe.

Shredder thinks he's Michaelangelo after a computer malfunction.

• In this episode, Krang is voiced by Townsend Coleman instead of Pat Fraley.

Aliens abduct Donatello and Rocksteady.

Title Reference: Invasion of the Body Snatchers

A visit to Earth from a Polarisoid results in havoc when Shredder (and later, April O'Neil) comes into possession of the alien's camera, because it does more than just take pictures.

• First appearance of Frip the Polarisoid.

Shredder and Krang engineer a love potion that makes Leonardo, Michaelangelo, and Raphael all fall in love with Irma. Donatello races for an antidote before Shredder drains a naval nuclear submarine of all its power, and things get crazy when Rocksteady takes a dose of the potion and falls in love with April.

• In this episode, both Krang and Burne Thompson are voiced by Townsend Coleman instead of Pat Fraley.

Baxter Stockman returns for revenge against the Turtles and Shredder, while our heroes attempt to stop Shredder's plan to siphon water from an underground reservoir.

Title reference: Return of the Fly

• In this episode, both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon.

An eager vigilante is causing a stir in the city, while Krang and Shredder take control of all the machines in the city. Maybe this new 'hero' can help the Turtles.

Notes: First appearance of Casey Jones. First episode not to feature Master Splinter.

A train accident produces gallons of mutagen that drench nearby cattle. The result is a super bull with a temper!

• In this episode, both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon.

White-collar criminals give new meaning to the term 'hostile take-over.' Casey Jones helps the Turtles uncover who's behind a new wave of corporate crime.

Michaelangelo gets a job as a pizza delivery boy. But who's his new boss?

Having had it with Bebop and Rocksteady's incompetence, Shredder and Krang use their technology to create robot duplicates of them, who are stronger and more intelligent, to keep the Turtles busy while they install a damaged mind-controlling Mesmerizer at the top of the broadcast tower at the Channel 6 building.

A skilled, and lovely, ninja warrior is hired by Krang to defeat the Turtles. Shredder's replaced, Leonardo's met his match.

• First appearance of Lotus.

Splinter suffers amnesia as the Turtles try to remind him that he is the true leader of the Foot Clan by reminiscing on their earliest adventures.

Notes: This episode is mainly a clip-show. Final episode where Krang is voiced by Townsend Coleman instead of Pat Fraley.

Our old friends, the Punk Frogs, are being terrorized by a mutant alligator in the Florida Everglades. Leatherhead teams up with Shredder to battle the Frogs and the Turtles.

Notes: First appearance of Leatherhead. In this episode, both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon. In this episode, Shredder is voiced by Dorian Harewood instead of James Avery.

It's Michaelangelo's birthday, but none of his older brothers seem to remember, and it frustrates him greatly. Meanwhile, Shredder and Krang discover what is possibly an "anti-mutagen" that, after testing it on three rock soldiers, can undo mutations. Shredder, Bebop and Rocksteady are sent to use it on the Turtles, and our heroes have a few close calls.

A rabbit ronin warrior from an alternate dimension is lost in our world. While the Turtles help him adjust, Shredder steals a dragon egg to unleash it on the city. Usagi Yojimbo's unwavering sense of bushido helps save the day.

• First appearance of Usagi Yojimbo.

Someone is stealing all the kimonos in the city. After Master Splinter's favorite kimono is stolen, April's famous detective aunt helps the Turtles retrieve it.

• First appearance of Agatha Marbles.
• Second Episode without Shredder and Krang as the main villains.

Shredder tricks Usagi Yojimbo into battling the Turtles.

Title Reference: Lassie Come Home.

• Final Appearance of Usagi Yojimbo.

Even a case of Turtle Pox cannot stop our heroes from an attempt to take down Shredder and Krang after they unleash Metalhead, a robotic fighting machine programmed to seek and capture the Turtles.

Notes: In this episode, Shredder is voiced by Dorian Harewood instead of James Avery. First appearance of Metalhead.

Leatherhead arrives in New York seeking revenge for his defeat only to run into the Rat King who captures him and reveals his plans for world domination. The two villains end up arguing, then finally fighting each other instead of the Turtles.

• Third episode without Shredder and Krang as the main villains.

Irma is kidnapped by Bebop and Rocksteady and is replaced by a robot that looks just like her that is programmed to eliminate the turtles. However, things seem a bit wrong as whenever the word "turtle" is said it instantly "zaps" whatever causes the word to be said with a laser. Meanwhile, the turtles try to rescue Irma from the Shredder's clutches.

Notes: Final episode where Raphael is voiced by Thom Pinto instead of Rob Paulsen. In this episode both Donatello and Bebop are voiced by Greg Berg instead of Barry Gordon.

The Turtles must clear their names when they are believed to be jewel thieves who stole a priceless emerald during a magic act run by a stage illusionist named Boldini.

• Final Appearance of Don Turtelli.

Zach's big brother, Walt, steals a rare pouch containing the only map to the Turtles' lair.

Bebop and Rocksteady put on an act to get the Turtles to eat cookies, but not any ordinary cookies, because these cookies could turn them into humans! Tempted to find out what being a human is like, Michaelangelo eats one and becomes one. While the effects wears off from time to time, they still kick back in. Meanwhile, the Turtles search for Michaelangelo with an antidote for the anti-mutagen before it destroys him, while Shredder's two mutant goons ask for help from their old gang to rob a ship. And during it all, April attempts to "join" the gang to get a story for Burne.

Title Reference: Hail, Hail, the Gang's All Here

Kala's pet Grybyx, which has a really bad temper whenever it gets hungry, escapes from Dimension X through a portal to Earth, causing trouble for the Turtles.

An impish alien comedian from Dimension Z (who has mannerisms similar to Pee Wee Herman), escapes to Earth to cause big trouble for the TMNT.

The Turtles enter an alternate universe in which they dreamed that they never existed, where Shredder rules the city as Shredderville.

Notes: In this episode, Shredder is voiced by Dorian Harewood instead of James Avery. Loosely based on the movie It's a Wonderful Life

An interdimensional alien spacecraft leads Baxter Stockman to his latest vengeful plot to destroy the Turtles and Shredder.

Notes: First appearance of spaceship computer. Final episode where Shredder is voiced by Dorian Harewood instead of James Avery.

After several failed attempts to get the Technodrome re-energized, Shredder and Krang run one last-ditch distraction for the Turtles at Fort Charles while Bebop and Rocksteady steal energy fuel cells from the neighboring space research center.

The Technodrome is up and running again, and it is up to the Turtles to hinder Shredder and Krang from getting to the surface.

After several setbacks, including firing a missile towards the turtles out at the South Dakota countryside, missing and instead blowing up Mount Rushmore, Shredder and Krang steal all of New York's electricity and charge it into a giant transdimensional gateway, designed to send Earth into Dimension X. The Turtles must defeat their enemies once and for all before Earth is destroyed by Krang's Rock Soldier army. At the end, the turtles send the Technodrome to Dimension X and are celebrated as the heroes in town.