With the Technodrome in serious need for new equipment, Bebop and Rocksteady are sent to Earth, disguised in human form, to capture the Channel 6 building and return it to Dimension X.

Professor Willard W. Willard, one of Donatello's idols, invents a Molecular Intensifier to control the growth of living things. Krang hears about it and sends Shredder to steal it. While testing the Intensifier, the Professor accidentally zaps his pet monkey Jocko, who grows to 30 feet in height. He also zaps some roots which then grow enormous and begin to take over the city, turning it into a jungle. Jocko gets attracted to April and starts chasing after her. To stop Jocko, the Professor zaps Donatello, making him 30 feet tall as well. Jocko gets angry at Donatello and they start fighting. The Turtles realize they have to stop Jocko before he and Donatello destroy the city. They urge the Professor to come up with a formula to reverse the Intensifier's effects. The Turtles finally reverse the Intensifier's effects. They stop Shredder from getting the device and return the City back to normal.

While trying to see the new toys at the Toy Fair, Michaelangelo stumbles upon a plot to take over a noted toy company.

In Dimension X, Krang watches on the viewscreen as April broadcasts from the opening of an exhibit of rare Chinese warrior statues, as well as the world's largest pearl. Krang thinks he can bring the statue to life and use the pearl to create a forcefield to bring the Technodrome back to Earth. Krang sends Shredder, Bebop and Rocksteady to the museum. They bring one of the warriors to life. Bebop and Rocksteady take it to the sewers to destory the Turtles. At the museum, Shredder brings to life the rest of the statues and orders them to find the Turtles and destroy them. Krang tells Shredder to order his statues to kidnap April and Vernon, luring the Turtles to the museum so the statues can destroy them. Bebop and Rocksteady lead the army of statues back to the museum with April and Vernon. The Turtles follow them to the museum hoping to rescue April and Vernon. The turtles realize that they won't be able to defeat the statues before Krang brings the Technodrome back to Earth.

New York is in the middle of an induced heat wave caused by Shredder, who must battle the Turtles and deal with his mother, Miyoko Saki, at the same time.

When General Tragg and his troops attack the Neutrino capital, the Neutrino leaders, Zenter and Gizzla, send their infant daughter Tribble through a portal to Earth, asking the Turtles to look after her, but Tribble causes big trouble for our heroes.

An eccentric billionaire, Monroe Q. Flem, who is also a collector, wishes to collect every piece of TMNT memorabilia that he can get his evil hands on, including April and the Turtles themselves.

Shredder, Bebop, and Rocksteady are in town to steal a rare new mutagen created by Oswald Dren, a grad student. Some mutagen is accidentally spilled onto a reel of movie film and monsters and a movie hero named Rondo come to life! The real Rondo is a wimp, and the Turtles try to help him confront the now-living monsters that stalk the street and the movie theater where the Monster Movie Marathon took place. With the turtles' help, Shredder and the mutants fail to steal the mutagen.

The Turtles must save the Earth from a massive energy drain and its Apocalyptic result by traveling to another dimension where turtles are the dominant species.

A Technodrome computer disguised as an electronic keyboard ends up on Earth, and in the most unlikely of hands.

When a power surge causes an arcade machine to release Tempestra, It's up to Leonardo to stop her digital wrath before she becomes dangerously powerful.

Gadget Man comes out of retirement after 50 years but is tricked by Shredder into fighting against the Turtles.

Krang hires a multi-dimensional ring-master who intends on making the Teenage Mutant Ninja Turtles part of his circus by using an anti-aging serum.

Vengeful Baxter Stockman and an A.I. computer return to Earth from a dimensional limbo and capture the Turtles while luring Shredder into their trap as well.

Raphael must contend with a mobster named Pinky McFingers when he is kidnapped from a local comedy club.

On their latest trip to Earth, Bebop and Rocksteady steal a machine that makes everyone scared of everything.

Raphael wins a place at the owner of a fast food chain's party. When the yacht is taken hostage by Hi-Tech pirates he and the mysterious lizard-woman Mona Lisa work together to stop them.

Bebop and Rocksteady use Krang's new Mutagen on Bebop's pet turtle Slash so he can do their housework for them. Slash runs away and is conned by an irritated entrepreneur into framing the TMNT.

A ray-gun makes Leonardo carefree and ignore his responsibilities. This leaves the Turtles defenseless and the city at the mercy of Maestro G Clef, a villain who destroys the city with music.

After many failed attempts from his rodent subjects to find food, the Rat King learns of an abandoned canister of mutagen lost in the sewers and claims it for himself. Then, he kidnaps Irma and Vernon and uses the mutagen to transform them into his mutant slaves, for the sole purpose of raiding food warehouses. It is later discovered that the mutations are unstable and can only be active if the Rat King plays his hypnotic flute.

When Michaelangelo decides to put one of Donatello's inventions on max power for his own entertainment, he ends in a--quite literally--little problem. April and Vernon get caught in the shrinking ray while getting footage of a military ship and join Michaelangelo on his wild adventure.

An alien called a 'Zipp' is sent to Earth, but this little alien soon becomes a big problem.

Donatello invents a machine that can freeze time, which a deranged professor steals as part of a plan to conquer the world.

Ninja Lotus Blossom's nightmares draw her to a strange artifact in the Turtles' possession. The artifact contains an angry spirit, whose wife's soul is within Lotus.

Dr. Polidorius, a mad scientist plotting to mutate all humanity into aquatic-beings, creates Ray (not the similarly-named Mighty Mutanimals character), who possesses several abilities of different marine species. Ray kidnaps April O'Neil, and Polidorius mutates her into a fish-woman to be Ray's mate.

The world's richest man announces a contest for the greatest superhero. The winner will receive an enormous diamond. Shredder and Krang enroll Bebop and Rocksteady for the contest to win the diamond. The turtles are incredibly surprised when they meet superhero contestants like Cheeseburger Man, Newsman (aka Vernon) and Rhino-man (aka Rocksteady) with his sidekick Mighty Hawk (aka Bebop).

Michaelangelo meets his favourite comic book hero after he saves a weakened Brick Bradley in the sewers, and then he and Bugman take on the evil Electrozapper together.

Michaelangelo must babysit and protect a young rich girl named Buffy, who knows the formula for a super fuel that Krang needs for the Technodrome.

Michaelangelo must rescue the other Turtles when they are captured by an evil scientist.

Shredder has a plan to destroy the Turtles, but with the Technodrome's portal out of commission, he is unable to challenge them on Earth, so he uses the Dimensional Teleporter to bring his enemies to Dimension X.

Donatello earns his degree from Sopho University, but discovers that he has been mistaken for a girl, so he asks Irma to masquerade as him. Meanwhile, the real Donatello discovers a plot by Professor Philo Sopho to destroy the Earth.

The Teenage Mutant Ninja Turtles are looking for some excitement. They soon find it when hoods start robbing fancy stores but only steal cufflinks! The turtles decide to investigate this and the only way to do so is to go as undercover crooks. After putting a competing gang 'on ice', the turtles get the scoop on the cufflinks and learn which cufflink they really want which is a high explosive and so the turtles must keep the hoods, and Shredder, Rocksteady, and Bebop away from it.

One night the turtles crash the video arcade to play video games all night. Leonardo's eye is caught by a video game called Tempestra's revenge. No matter how good of player, Leonardo is, he always loses to Tempestra. But things get much worse after the video game comes to life and Tempestra breaks free. She needs an awful lot of energy source in order to continue to exist.

Splinter has suddenly disappeared, and a note left behind from him forces the Turtles to go their separate ways, but one by one, they are captured by Leatherhead and the Rat King.

A machine called the Transmogrifier causes Raphael and a cab driver to swap bodies, and it is later discovered that a defect in that same small device could do some very big damage to the city if activated.

While trying to contact the Turtle Nebula, Donatello meets an intelligent lizard alien named Algernon ('Algae' for short), who must help him and the other Turtles rescue April from a greedy man named Hostile Hiram Grelch.

A failed mutagen experiment results in an invasion of giant insects and arachnids in New York City.

A Foot Soldier named Alpha-1 has his intelligence increased, but it results in a Foot Soldier rebellion against Shredder and Krang and the duos exile from the Technodrome.

While helping April investigate a report of giant monsters attacking a superstitious farming village, Leonardo is mistaken for an alien from another planet. The lone Turtle must avoid being hunted down into extinction while also trying to rescue April from a mad scientist.