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.
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 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
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.