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. Note: This is the final episode in which Michaelangelo uses nunchaku as his main weapon rather than a grappling hook.
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. Note: First appearance of Professor Sopho.
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. (This is the only episode appearance of Baxter Stockman's twin brother Barney Stockman.) Note: First appearance of Pinky McFingers.
Casey and Leo investigate a series of large-scale robberies. Not surprisingly, Hun and the Purple Dragon are to blame. However one of their hauls is a crate that should never have been opened!
Casey and the Turtles are practising their hide-and-seek skills at an abandoned warehouse complex. All the while, a strangely familiar figure watches them from the shadows - with an army of rats at his command!
Raphael wins a place at the owner of a fast food chain's party. When the yacht is taken hostage by high-tech pirates, he and the mysterious lizard-woman Mona Lisa work together to stop them.
Frustrated with his bossy nature, Raphael and Michaelangelo accidentally shoot Leonardo with the personality modifying ray, turning him into a fun loving 'dude' who neglects his responsibilities. Donatello, Raphael and Michaelangelo must stop Maestro G. Cleff from destroying the city.
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.
Ninja Lotus Blossom's nightmares draw her to a strange artifact in the Turtles' possession. The artifact contains an angry spirit, whose dearest wife's spirit/soul is lying deep within Lotus herself.
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.
Usagi and Gen come to New York for a visit with the Turtles. Gen gets a little carried away by the bright lights of the big city and goes wandering off on his own. And if the modern world wasn't dangerous enough, an assassin from Usagi's world has followed Usagi and Gen. His target: Leonardo.
It is time for Leonardo to move on. Splinter sends Leo to a new sensei, or rather, a very old sensei. The journey is long and perilous. Can Leonardo look into himself and find the right answers to his questions? Can he even find the right questions?
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.
Rich tycoon J. Gordon HungerDunger runs a contest for the best superhero, with a phony diamond as a prize, to cover up a scheme to hypnotize the world. Even the Foot Clan gets suckered into this contest, with Bebop and Rocksteady dressing up as superheroes so they can win the diamond, and use to power up a laser Krang has created.
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.
The Turtles must baby-sit and protect a young rich girl named Buffy Shellhammer from Shredder and Krang, as she knows of a formula for a super fuel needed for the Technodrome.
When the power goes out in their lair, the Turtles and Splinter gather around the candlelight as Leonardo tells a story he learned from the Ancient One about Splinter's sensei, Hamato Yoshi.
Leonardo becomes addicted to a new arcade game, Tempestra's Revenge, which ends up affecting his usual routine. But when a freak power surge releases Tempestra from the cabinet, Leonardo has to stop her digital wrath before she becomes dangerously powerful. Note: First appearance of Tempestra.
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.
With the outbreak-mutant situation the Turtles feel they have to deal with and Donatello sick his brothers leave him with Casey and April for care. But Donatello is not sick but in the last stages of a second mutation.
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 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.
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.