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

Leonardo, Donatello and Raphael are enjoying an episode of professional wrestling when Michaelangelo enters the room and turns the channel to 'ON TRIAL' hosted by Clayton Kellerman, a Morton Downey-like rabble rouser who suggests that a clear and present danger is lurking in the sewers: Teenage Mutant Ninja Turtles. The Turtles are aghast and can't understand why people would hate them. April has her make-up department make human masks so the Turtles could move more freely in the streets. Meanwhile, Shredder is sweating from the heat, as Krang "chews him out" for his failure to retrieve the necessary components to repair the refrigeration units. Shredder has had enough and suggests that Krang go up on the Earth's surface and get what he needs and eliminate the Turtles himself. Krang considers this a good idea.

While preparing for Irma's birthday party, Michaelangelo realizes he has forgotten to invite the guest of honor. He contacts April, who is in the midst of interviewing Professor Von Zifflein about the discovery of a meteorite that "just crashed in the area." The professor claims that this is a very unusual meteorite with a core composed of an extremely rare isotope known as 'Exaporon'. The Turtles turn on their TV to watch their favorite journalist as she interviews the professor. Suddenly a noxious gas fills the room and someone steals the meteorite. Before the thief can escape, he stops in front of the news camera, revealing himself to be Shredder.

It was a dark and rainy night. The Turtles, wearing their trench coats and fedoras investigate a reign of mob terror. Donatello, in his worst 'Sam Spade' impersonation, narrates this pulp/film nor story of banks all over the city being "taken down by the mob". But, as Donatello tells the viewer, the mob is using sophisticated weaponry -- the kind that could be only supplied by Shredder. And what mobster would be 'gutsy' enough to deal with Shredder?

The Turtles go flying when the Shredder invents a gravity-altering device.

Mr. Thompson orders April into his office to assign her a news story. It seems that the nightwatchman at Cybertech Laboratories spotted "some weird character hanging around" -- Mr. Thompson is convinced that he must be a friend of 'April's Turtles'. She assures him that he is not and heads off to Cybertech Lab with mini-cam in hand. Meanwhile, down in the Turtles' Lair, Donatello is displaying his new Super Pizza Maker. The other Turtles are impressed with its ability to make pizza in a matter of seconds, but when it is switched into high gear -- the machine overloads and explodes, causing loose parts to scatter across the room. One of these 'loose screws' hits Leonardo, causing "just a bruise". Suddenly, April contacts them from Cybertech Labs, via the Turtle Com, to inform them that Shredder, Rocksteady and Bebop are up to no good. While she waits for the Turtles to arrive (including Splinter, who is concerned about Leonardo's injury,) April begins to videotape Shredder and his goon.

In the middle of a summer heat wave, the Turtles cool down by having pizza at Plink's, home to the world famous chef: Wolfgang Plink. Suddenly, three Punks storm into the restaurant and try to hold the place up. Only they did not count on the Turtles, who dispatch them with ease. Back at Channel Six News, April, Vernon, Irma, and Mr. Thompson finish watching a tape of April's broadcast. Mr. Thompson is upset because there was no footage of the Turtles. April tries to explain that she promised not to include it in her report. Mr. Thompson is furious. In his day, he goes on to explain, a good reporter let nothing stand in his way of getting the news. Vernon chimes in by suggesting that if Mr. Thompson were not so old and fat, he would be out on the streets now searching for the Turtles. The insulted Mr. Thompson thinks that this is a great idea and volunteers Vernon to go with him, leaving April to cover a story on why the air conditioners all over the city are on the blink.

Dressed in their human disguises, Donatello and Raphael venture out of their Turtle lair to buy supplies to make pizza. On their way back, via what they believe to be a shortcut, they are "intercepted" by a gang of young street Punks. Suddenly, a young boy wearing a Turtle costume, and who calls himself Zack: "Master Ninja Turtles and the Scourge of Evil Doers", drops in out of nowhere. As he prepares to defend Donatello and Raphael, he falls flat on his face, allowing the real Turtles to dispatch the punks with ease. Afterwords, Zack explains how he wants to help them fight crime -- but Raphael tells him that he is more of a menace than a crime fighter. The kid leaves in a huff, picking up Donatello's Turtle-Com -- which he had lost in the scuffle with the would-be attackers.

After an unpleasant encounter with a rat, Mr. Thompson assigns April to research the growing rat infestation. April heads for the sewers and after turning up nothing returns to Channel Six News to meet her deadline. However, she and Irma are forced to return to work on foot after all four tires of the Channel Six News van have been chewed by rats. Suddenly, they are being pursued by an army of rats and escape on a passing city bus. Back at Channel Six News, in the middle of April's editorial, the lights go out. When they come back on April is gone. The Turtles, who were watching April on TV in their secret lair, spring into action to locate their missing friend.

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.

Emperor Aleister of Malicuria comes to New York City, bringing along a shard of Lydium 90 to the USA. In order to get the mineral to fuel the Technodrome, Shredder invades the costume party thrown by the Malicurian US Embassy to kidnap Aleister's daughter, princess Mallory, but ends up capturing April in a fancy dress who looks just like Mallory.

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.

Krang's computers detect an alien metal on the surface of the Earth, so naturally, Krang sends Shredder, along with an Alien Metal Detector, to the surface to find it. Meanwhile, the Turtles realize that it is National Sensei Appreciation day and they must go out and buy Splinter a present. Later, at the pawn shop, the Turtles, dressed in their trench coats and fedoras, purchase an old ninja sword. As they leave, Shredder, Rocksteady and Bebop arrive, via their Transport Module, at a Laundromat across the street. Krang's Alien Metal Detector begins 'sounding', indicating that what they seek can be found in the pawn shop -- but when they arrive, the signal weakens. Shredder is convinced that the 'Four Men' who left the shop before they arrive, possess the 'Alien Metal'. When the pawn shop proprietor tells him that they purchased a sword -- Shredder is even more convinced.

Still searching for a way to destroy the Turtles, Krang develops a Super Pump that he intends to use to flood the sewers and flush out the 'boys in green'. After sending Shredder, Rocksteady and Bebop to make the necessary preparations, Krang begins pumping water out of the ocean and pumping it into the sewers. Meanwhile, in the Turtles lair, Splinter and the Turtles are in the middle of a pizza repast when they are swept away by the sudden onslaught of water. But back down in the Technodrome, something has gone wrong. Krang's pump can not be shut off as more and more water is being sucked from the ocean and "dumped" into the sewer -- which is now overflowing into the streets. Soon, the entire city will be underwater.

After awaking from a nightmare in which he failed himself and his comrades in a battle against Shredder, Leonardo feels that he is unfit as a leader and, donning civilian clothes, decides to leave the Lair and the Turtles. Meanwhile, Shredder and Krang have left the Technodrome and are on the top floor of the Mile High Tower, executing Shredder's new scheme for world domination. This time out, he has created a Solar Siphon and by aiming it at the sun, he can effectively drain the sun's 'power/energy' and store it in compact batteries while the Earth slowly goes into a deep freeze. Everyone will be too cold to resist him.

At the local Mardi Gras parade, April, dressed as a 17th-century noblewoman "right out of the Three Musketeers", suggests that the Turtles, who are walking the street 'au natural', should be in costume and should also read Dumas' book. She just happens to have a copy on her and gives it to Leonardo, who reads it at the first opportunity, is enthralled by it and tries to convince the other Turtles of the striking similarities between themselves and the Three Musketeers. Meanwhile, down in the Technodrome, while watching April O'Neil's coverage of the Mardi Gras parade, Krang learns that the priceless Star of Brazil diamond, is, in fact, the long lost element of Impervium - a substance found only in Dimension X and was 'sent' to earth as part of an experiment. Krang tells Shredder that with the Impervium once again in his possession he could create weapons unknown to the likes of man. Shredder wastes no time sending Rocksteady and Bebop up to the Earth's surface to steal the gem.

April covers the launch of a new system developed by the city to help clean up the city's garbage problems faster than ever: An automated computer, programmed to retrieve all forms of waste material, controls several garbage pick-up trucks from its control center, Shredder sees this computer as an ideal weapon to use against the turtles. Breaking into the lab where the computer is situated, the villain re-programs the c.p.u to capture TURTLES rather than retrieve litter... However, things go awry when all the trucks pick up are any non-mutant turtle they lay their eyes upon..including the last of a soon to be an extinct race of turtles, just about to give birth.. Can the green machine save their 'distant cousins' from this terrapin-taker? Or will Shredder get what he originally wanted after all?

Shredder has an accident and ends up acting like Michaelangelo. The episode has the Turtles dealing with him switching between his evil personality and Michaelangelo, to hilarious consequences.

The Turtles throw April a surprise party to celebrate her first anniversary as a reporter at Channel Six News, but April is not feeling very celebratory -- it seems that Burne Thompson has suggested that she will not be celebrating her second anniversary if she does not find a story soon. Donatello and Irma rush out to get a special pizza in an effort to lift her spirits. Meanwhile, Krang and Shredder send Rocksteady and Bebop up to the Earth's surface to locate "a new source of energy generated by the Nucleon Fission Reactor at the University". But the mutants think that Shredder is sending them 'fishing' and when they finally learn their mistake, a bright ray of light, coming from out of the sky, zaps Rocksteady and he disappears.

After demonstrating poor skills in their daily katas, the Turtles convince Splinter that they need a vacation -- he agrees, if they can agree where to spend it. Meanwhile, an Alien Tourist/Polarisoid arrives on Earth taking photos of everything -- and everything he takes a photo of disappears right into his camera, to be viewed by family and friends back home on Polaris. Calls are flooding into Channel Six News -- even City Hall is missing and April sets out to get an exclusive. At the Technodrome, Shredder and Krang realize that if they could get hold of the Polarisoid's camera they could rid themselves of the Turtles once and for all.

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 submarine of all its power.

Noticing that the Technodrome's ballast tanks are low, Krang decides to take the Technodrome closer to the surface so that it can siphon off water from an underground reservoir. Meanwhile, Donatello has built a device that will track the Technodrome's movements. No sooner is he done, then the Technodrome is on the move. Observing the action of both the Turtles and Shredder and company is none other than Baxter Stockman/The Fly, who has recently returned to the current dimension and is desperate to enact his revenge on both Shredder and the Turtles. The Turtles, along with April, arrive at the underground water tank before Shredder, and while they prepare for him, April is kidnapped by Baxter Stockman/The Fly.

A self-appointed vigilante, wearing a hockey mask and named Casey Jones, is striking fear in the hearts of the city's criminals. However, the legal system feels that this same vigilante is violating the civil rights of said criminals, therefore, the Police, who believe that the Turtles are responsible, issue an All Points Bulletin. Mr. Thompson calls April at her apartment at five in the morning to assign her the story -- she accepts, but only to prove the Turtles' innocence. The Turtles have also had their own run-in with the vigilante and, realizing how easy it will be for people to confuse him with them, elect to try and stop him. Meanwhile, Krang has developed an army of tiny mechanical insects designed to infiltrate the city's machinery, thereby having access to control it.

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

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?

Shredder and Krang produce hi-tech versions of Rocksteady and Bebop to keep the Turtles busy.

Krang hires a female Ninja, Lotus, to replace Shredder. It seems that Lotus has agreed to help Krang locate the Turtles in exchange for 100 pounds of gold. To prove her worthiness, and Shredder's unworthiness, Lotus defeats him with her Ninja skills. Shredder, Rocksteady and Bebop leave the Technodrome with their tails between their legs vowing that Krang will someday beg to have them back. Meanwhile, Burne assigns April and Vernon to do a special story on romance. At the Olaf Perfume Factory, April interviews a Monsieur Olaf, who reveals that he has a 'Scent Analyzer' that can 'sniff out' any fragrance. But, while protected by three armed guards, is suddenly stolen by Lotus and in its place, she leaves a lotus flower. A short time later, Lotus visits Aqua Land and steals from Dr Gilman, a marine biologist, his complete file on his study of genetic codes of turtles. Once again she leaves a lotus flower in its place.

Krang and Shredder are going stir crazy. They have been defeated once too often by the Turtles, so Shredder has decided to do something about it. He takes Rocksteady and Bebop up to the Earth's surface and to the Asian-American Cultural Center where the burial urn of an ancient noble warrior and founder of the Foot Clan, Shibana-Sama, is on display. Meanwhile, April is doing a live broadcast from the same Asian-American Cultural Center. Splinter suggests that he and the Turtles should hurry there at once for fear that Shredder may be on his way. But they are too late. Shredder knocks the Turtles out with a ninja smoke bomb and releases the spirit of Shibana-Sama. Shredder requests that the Warrior Spirit teach Rocksteady and Bebop the secret ways of the ninja and make them invincible. Shibana-Sama replies that only the true leader of the Foot Clan can make such a request.

While Raphael is reliving the past, via the Turtles' photo album, their Frog friends in the Florida Swamps (Napolean Bonafrog, Genghis Frog, and Rasputin) are being terrorized by a mutant alligator known as Leatherhead, who makes them his slaves. They decide to call the Turtles for help. Meanwhile, Krang's scanner picks up Leatherhead's activities and he sends Shredder, Rocksteady and Bebop to the same Florida Swamp to retrieve the mutant alligator and use him to help defeat the Turtles. But no sooner do the Turtles and April arrive when they are captured by Leatherhead. The Frogs turn the tables and help the Turtles capture Leatherhead. Shredder and company arrive in the Florida Swamp and stumble upon the Turtles and April, the Frogs and Leatherhead. They decide to track them for awhile before charging in and attacking. Sure enough he finds his golden opportunity when he rescues Leatherhead from the quicksand that the Turtles, the Frogs, and Leatherhead have fallen into.

It's Michaelangelo's birthday, but none of his 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.

Thanks to a run-in with General Traag from Dimension X, the Turtles discover that Krang is experimenting with his 'Dimensional Portal' again. Donatello decides to contact the Nutrinos in an effort to discover what Krang is up to. Donatello's 'Pan-Dimensional Portal' is knocked 'off track' by Krang's machine and instead of Dimension X, the Turtles make contact with an alternate Earth, in 16th century Japan, where animals are the dominant species -- not humans. Suddenly, a samurai rabbit named Usagi Yojimbo is 'sucked' through the portal and into the Turtles' Lair. After a short battle, Usagi admits defeat and begs to learn their ninja secrets.

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.

Shredder tricks Usagi Yojimbo into battling 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 in an effort to destroy the Ninja Ts. But first, in order to program the robot, Krang needs a 'Brainalyzer' scan of the Turtles. Shredder, Rocksteady and Bebop travel up to the surface and force the Turtles out of hiding by breaking into various business establishments throughout the City. Sure enough, the Turtles arrive at the scene of the crime, allowing Shredder to zap them with the Brainalyzer and making good their escape. The Turtles are confused but relieved to be back at home in their beds.

Leatherhead heads to New York to get revenge on the Teenage Mutant Ninja Turtles. He runs into the Rat King instead, who has stolen a truckload of chemicals and plans to turn the citizens of New York into mindless zombies so his minions of rats can rule the city. With two of their most insidious foes in the same sewer, the Ninja Turles must work with April O'Neal to stop them both.

Rocksteady and Bebop, on Shredder's orders, kidnap Irma, who pleads with them to wait until tomorrow -- it seems that she has a date with a handsome weatherman from Channel Six News. As soon as April discovers Irma has been abducted, she contacts the Turtles. At his secret hideout, the Shredder activates his 'Turtle Terminator' to replicate itself to look just like Irma. He then sends the Irma/Turtle Terminator out on its mission -- to destroy all turtles. Irma/Turtle Terminator returns to Channel Six News and professes that nothing has happened to her nor has she seen Rocksteady and Bebop. April reports to the Turtles that Irma is back and that everything is fine but the Turtles are doubtful. They continue to investigate. However, when Irma/Turtle Terminator overhears Burne Thompson refer to his girlfriend as a 'turtle dove' she fires a laser blast out of her eyes, melting the telephone. April realizes that something is wrong.

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 wizard named Boldini.

Zach, the 'fifth Turtle' and his brother Walt visit the Turtles. As they leave, Walt takes a map that could guide Shredder to the lair... if it happens to fall into the wrong hands. Bebop and Rocksteady find out about the map by eavesdropping on Zach and Walt. Shredder, Bebop and Rocksteady pursue Zach and Walt through a Science Fair. Walt tries to look for a place to hide the map. Meanwhile, Zach gets captured by Shredder and gets taken to the Technodrome. Walt tries to find the Turtles to inform them of what has happened to his brother. April is broadcasting from the Science Fair and notifies the Turtles that Walt was seen being chased by Shredder through the Fair. The Turtles set out to find them and on the way they run into Walt who is fleeing from Shredder. Back at the Technodrome, Zach is driving Krang crazy. He is playing with all the buttons on the console. The Turtles find out where Zach is and rescue him, making Krang very happy.

Shredder tries to trick the Turtles into eating cookies made with anti-mutagen. The mutagen is supposed to change the Turtles into human weaklings so Shredder can destroy them. Donatello discovers what the cookies are made of and throws them away warning the Turtles that the mutagen is unstable. Michaelangelo wanting to be a human, tries one of the cookies and it mutates him into a teenager. As a human, he meets with April who is working undercover in a gang. This gang, lead by Lugnut, happens to be the one that Rocksteady and Bebop used to belong to. Bebop and Rocksteady ask them to steal electronic parts from an abandoned tanker for the Technodrome. Michaelangelo is having problems with the mutagen being unstable. He keeps changing from human to Turtle at the most inopportune times. April sees him at one of those times and discovers who he really is.

An affectionate, cuddly creature from another world shows up on Earth, with the ability to move objects by mental power. It turns out to be an escaped pet of the Neutrinos. The Neutrinos - Dask, Kala and Zak are in search of Kala's pet Grybyx. As it turns out, the small and cuddly creature can turn into a humongous monster. This transformation occurs when it gets fed pizza, and soon enough the gigantic Grybyx-creature threatens the Turtles and the city. Of course, Shredder and Krang want the Grybyx, but they end up getting more than they bargained for. After transforming back into its old self, the Neutrinos return the once-again cuddly little creature to their dimension.

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 have entered an alternate universe in which they thought had never existed and The Shredder rules the city as Emperor.

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

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.