The intentions of the Ninja 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.
The personalities 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.
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 land frozen in a stage where dinosaurs roam the land.
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 has created a computer disk holding all available information about Michaelangelo who, at that moment, had eaten every pizza in the lair, forcing Splinter to hypnotize him into craving pizzas no more. Meanwhile, when Shredder attempts to extract information from the disk, there's a malfunction, and Shredder obtains Michaelangelo's personality, while the genuine article is captured by Rocksteady and Bebop.
Shredder and Krang engineer a love potion that makes Leonardo, Michelangelo, and Raphael all fall in love with Irma. Donatello races for an antidote before Shredder drains a naval submarine of all its power.
The Shredder opens a pizza parlor "Weird Pizza" in his latest scheme to catch the turtles. He intends to place a homing device disguised as an anchovy on a pizza, then as soon as the turtles call in with their order and the pizza is delivered, he will send an army of Foot Soldiers into their lair. All he needs is a delivery boy and he ends up hiring the most unlikely candidate: Michaelangelo. This hip turtle is looking for a job so he can buy a new belly board. Not knowing he's really working for Shredder, he jumps into action, and "borrows" the Nutrino Starcruiser. ...
It's Michelangelo'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.
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.
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.