April O'Neil, ace reporter for Channel 6, investigates recent break-ins, allegedly by Ninjas, which have resulted in the thefts of numerous technologies, however, a chance encounter with a gang of theives soon leads her to a bigger story when she is saved from the criminals by four Ninja trained, mutated Turtles. The Turtles take April back to their lair, and, after getting better acquainted, April learns they are good hearted mutants, they decide to investigate the thefts together, and their efforts lead them into an encounter with the mysterious ninjas, The Foot Clan, and thier leader, Shredder

The Shredder kidnaps Splinter in an attempt to lure the Turtles to his own cause, in order to rescue Splinter, the Turtles must enter the Shredder's mobile fortress, The Technodrome and brave it's dangerous weaponry, and even if they can do that, they must still confront The Shredder himself, who is armed not only with the nature of their origin, but also with his own mutated henchmen, Bebop, and Rocksteady.

Baxter Stockman, a mad scientist, is showing an exterminator his new invention a rat catching robot called Mousers. The exterminator rejects Stockman's offer however shredder decides to buy his inventions. He unleashes a dozen mousers in the sewers they are easily defeated by splinter but is no match for 1200 the turtles track to the one responsible for the mechanical rats to his hide out while there Michelangelo encounters Krang.

Shredder experiments with the Inter-Dimensional Portal, hoping to contact Krangs' Rock Soldiers and prepare an invasion of Earth, but a group of fun-loving aliens called the Neutrionos, renegades in Krang's dimension, take advantage of the Portal's opening and use it to arrive on Earth, and they eventually run into the Turtles...

As Shredder lures Splinter into The Technodrome, this time with the promise that a weapon in his possession can restore the sensei to human form, the Turtles confront a giant-sized Krang, now in a new body, in the heart of New York City, the final battle results in Splinter sacrificing his chance for normalcy to save his students, the five then battle the invading Dimension X troops inside The Technodrome, resulting in the banishment of the fortress, and it's insidious occupants, into Dimension X itself.