When April O'Neil wakes up in the Turtle's lair she has major trouble dealing with the reality of four giant talking Turtles and a Zen-master rat. She soon learns of the origin of the Teenage Mutant Ninja Turtles and they realize their common enemy is Baxter Stockman and his army of robotic Mousers.

Raphael is a little cooped up underground with only his brothers and Master Splinter. When Raphael almost clobbers Michelangelo in some brotherly sparring, it's apparent that Raphael needs to get out ... let off a little steam. But when he meets up with Casey Jones, a vigilante erring a little to the right of justice, Raphael must face the reality of his own hothead ways...

After Casey Jones makes himself an unwanted guest in the Turtles' lair, Raphael takes him topside for a "breath of fresh air", where they encounter the Foot Tech Ninjas.

On a nightly training run, the Turtles and Casey Jones break up a Purple Dragon robbery. One of the perps is Angel, a girl Casey knows from the neighborhood who's going through her initiation rites to become a Purple Dragon.

Oroku Saki (aka the Shredder) attempts to convince Leonardo that Saki is fighting the good fight ... that he's out there carrying on the great tradition of Bushido and Ninjitsu, and the turtles should stand with him.

On a training run Leo is ambushed by a major Foot attack force, including Foot Tech Ninjas, their old enemy Hun, and a new threat: the Foot Elite!

When the Foot Ninja attack April's apartment in force, the Turtles fight against overwhelming odds to get the wounded Leo to safety.

The Turtles, Splinter, Casey and April just barely manage to escape from the explosion that destroys the antique store. They hit the road and hide out at Casey's grandmother's old farmhouse, but Leonardo is badly wounded.

The Turtles return to New York with one goal in mind: to destroy the Shredder once and for all.

The Turtles and Splinter continue to fight their way up through the Foot Headquarters skyscraper, facing down three misshapen Mutant Shredder Clones, a hallway of traps, and the Mystic Ninja.

With Stockman showing up in the middle of the final battle between our heroes and the Shredder, everything is thrown into chaos ... so much so that our heroes must join forces with the Shredder and Hun to defeat Stockman.