A professor's new ray-gun causes plants to go wild and his pet ape Jocko to become a giant rampaging monkey. By using the same ray-gun, Donatello is increased to Jocko's size so he can fight the giant ape and save April from him
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.
J. Gordon Hungerdunger, a Texas millionaire, is holding a "best super-hero" contest. The winner of the contest will receive the humongous Malaprop Diamond. No one is aware of it, but Hungerdunger is using the contest as a diversion so that he can put a zombie-making chemical into the city's water supply. The malevolent millionaire figures that if he can get the citizens under his control, he can easily take over the city
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 Michelangelo 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 Michelangelo on his wild adventure.
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.
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 excitment. 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.
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
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 (based on the Hare character from "The Tortoise and the Hare").
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.