After a fight with Shredder causes Donatello to be struck by a laser beam, his personality changes to become a costumed superhero known as the Dark Turtle. His mission: Seek out & destroy Shredder. Meanwhile, a dinosaur-like alien race called Triceratons, invades Earth.

A small alien being, named Quirx, crash-lands on Earth, with intergalactic stormtroopers in hot pursuit. The Turtles must figure out how to get Quirx back to his home planet, before Earth is destroyed.

Shredder uses a time machine to travel back to Ancient Japan in the year 1583. He plans to defeat Hamato Koji, the man who founded the Foot Clan, and Splinter's great ancestor, for if Hamato Koji is defeated, then Master Splinter would never have been born and the Turtles would forever remain ordinary turtles.

Two convicts from Dimension X are brought to Earth when Donatello's Portable Portal Generator malfunctions.

While Splinter's sensei, Mogo-san, is visiting New York, a criminal gang of ninja, known as the Black Heart Gang, are terrorising the city with a crime spree, and Mogo-san's grandson, Yoku, is their leader.

In an attempt to finally defeat the Turtles once and for all, Shredder assembles Leatherhead, Tempestra, Scumbug, Chrome Dome, Antrax, The Rat King and Slash to form a team that proves too much for the TMNT.

The Neutrinos return and assist the TMNT in keeping a new invention out of Krang's clutches.

Kerma the space turtle returns once again for the Turtles help in programming his city's new defence robots but Groundchuck and Dirtbag have also returned to the city to cause trouble

Baxter Stockman & his alien computer return to Earth from the Dimensional Limbo & take possession of Shredder's Retro-Mutagen Ray Gun.

The Turtles discover an Atlantean city, not in ancient Greece, but in modern times. After meeting a merman who, in reality is the true King of Atlantis, the Turtles must defeat Shredder & dethrone Bebop, who been set up as a puppet king

Professional mutant hunter Dirk Savage is conned into to rounding up New York's mutants, Tokka, Rahzer, Two of the Punk Frogs, Leonardo, Michelangelo and Mondo Gecko all fall prey and become part of a mutant slug's army

In order to defeat the Turtles, Krang creates 6 clones of himself to deal with them. But, when the clones start to think for themselves & Krang loses control, the Turtles must save the city.

A new amusement theme park has opened with Shogun, Medieval & Future themed attractions. The Turtles are invited to try out the attractions, but when the robots in the park start to play too rough, the Turtles are in big trouble.

After bringing the Technodrome back to the surface, Shredder and Krang trap the Turtles and send them to Dimension X where they become slaves. In the meantime, Shredder and Krang back on Earth once again try to take over the world.