In their underground lair deep beneath the city streets, in the middle of an intense training session, the Turtles and Master Splinter are suddenly attacked by a horde of Mouser robots! These mechanical menaces chomp through everything: stone, steel... Turtles! In the course of the battle, the Mousers cause the roof of the Turtles' sewer-lair to cave in, separating our heroes from their beloved Master. Now the Turtles must abandon their home of 15 years and find their missing Master. But on the way, they have to deal with collapsed sewer tunnels, the Purple Dragon street gang, and a small army of mysterious, highly trained Ninja!

The Turtles discover the source of the Mouser robots that trashed their old lair: Dr. Baxter Stockman a noted technological genius/inventor, who tries to pass off the Mousers as a means to eradicate the city's rat problem. Donatello gets one of the broken Mousers working and the Turtles chase it through the sewers. Meanwhile, Stockman's lab assistant April O'Neil uncovers a secret subterranean facility where hundreds of Mousers are being manufactured and stored - but to what end?

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...

When a scientist accidentally unleashes a super-powered Nanotech monster with a childlike mind, it adopts a small-time thief as its father figure, and the mayhem begins! Their crime spree targets April's new antique shop, and the Turtles come to her rescue. But how do you stop something that rebuilds itself as fast as you bash it apart? It's a question the Turtles better answer fast, cause the Nano-matic slices, it dices, and it purees turtle soup in seconds!

The Turtles, investigating a strange blackout, discover the Foot Ninja stealing a Japanese ceremonial sword from the Museum. But this is no ordinary sword. And just what do the Foot intend to do with it?

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 - enhanced soldiers able to turn themselves invisible. Raph is caught and interrogated, but Casey manages to slip away and warn the others. Raph escapes his captors but, unbeknownst to him, is tailed by a squad of cloaked Foot Tech Ninjas. Will Casey and the others get to Raph in time before he leads the Foot directly to the Turtles' lair?

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. Casey tries to stop Angel from going down the wrong path, but ends up getting captured by the Purple Dragons and offered up as the "prize" in the gang's fight club competitions. It's up to Angel to bring the Turtles in to help rescue Casey. The Turtles must battle it out against the biggest, meanest Dragons, including Hun, their man-mountain of a leader.

The boys have made friends with a group of homeless, and are worried when they start mysteriously disappearing into the night! Some Turtle-style detective work leads them to the Garbageman, an immense, smelly egomaniac, who is kidnapping the homeless for slave labor to build an empire on a foundation of garbage. Sounds like it's time for the Turtles to take out the trash!

Shredder attempts to convince Leonardo that the Foot are fighting the good fight and the turtles should stand with him. Leonardo is taken in and almost convinces the others until Splinter reveals what he knows of the Shredder. Leonardo realizes he's been fooled - it's never a good idea to fool a turtle at least not a Teenage Mutant Ninja one...

Our four turtles stand facing their most formidable foe to date - the Shredder. Battle weary, the turtles cannot stand against the Shredder and manage to slip away getting separated in the process. Can they survive apart? Can they get back together in time to save themselves and face the Shredder? Maybe with Master Splinter there to guide them...

Believing the Turtles can accomplish so much more for the city, and inspired by iconic superhero Silver Sentry, Michelangelo decides to take a crack at being a superhero. But he soon discovers superhero-ism is not all it's cracked up to be. Worse still, he stumbles upon a mind-control experiment by Silver Sentry's arch nemesis Dr Malignus!

When Don's examination of some mysterious crystals attracts the attention of a subterranean monster, the Turtles underground exploration unearths a Foot Genetics Lab! A video record of strange experiments reveals more of Shredder's mysterious agenda, but when the mutants attack, the boys better watch out, or it's everybody out of the gene pool!

After discovering an abandoned underground Foot Genetics Lab, and being attacked by the once-human Quarry, the Turtles assist them in trying to repair a force field to protect them against the mindless beasts roaming the tunnels. But the force field needs a new crystal power source, and the only place to get one is by travelling deeper underground, to the seemingly haunted catacombs, where many have mysteriously vanished...

When the Turtles and their new allies start vanishing one by one, only Michelangelo is left. He finally finds the perpetrator in the underground city - it's sole survivor. Though his intentions appears noble at first, by restoring the creatures to their normal human selves, there is a catch...

With all the turtles living in April's apartment, things are getting a little crazy. Donatello meets up with Kirby, an artist renting April's basement apartment. Through the powers of a mysterious crystal tied to his pencil, Kirby is able to create anything he draws including his own world - a world that he and Donatello get sucked into where things get more and more curious.

On a training run Leo is ambushed by a major Foot attack force, including Foot Tech Ninjas, Hun, and a new threat: the Foot Elite! At their temporary home at April's apartment, Don, Raph and Mikey tire of wait for Leo to get back and decide to go look for him. But is it too late?

When the Foot Ninja attack April's apartment in force, the Turtles fight against overwhelming odds to get the wounded Leo to safety. The Shredder raises the stakes, trapping our heroes in the burning Antique Shop with no way out!

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, drifting in an out of consciousness. As he attempts to recover, the Turtles and Splinter tell tales of Leonardo's early adventures, using the stories to help guide him back to the real world.

Still recuperating up at Casey's grandmother's farm, the turtles are feeling the sting of boredom. However, a scientist known as the "Monster Hunter" has come to the area searching for a legendary monster, rekindled by the sighting of a green monster lurking in the woods. So Casey, Mike and Don decide to have a little fun with the Monster Hunter. It all becomes a bit odd when the boys find some other large green creature besides themselves lurking about. Can they survive both monster and Monster Hunter?

With Leo fully recovered the goal is clear: to destroy the Shredder once and for all. With April providing remote computer assistance, the Turtles begin their assault on the Foot HQ skyscraper, fighting their way to the top floor by floor. They battle an army of Foot Ninja Guards and the deadly cloaking Foot Tech Ninja. But no one is quite prepared for what they encounter inside a Foot Genetics lab...

The Turtles and Splinter continue to fight their way up through the Foot Headquarters skyscraper to face the Shredder. But they now have to face off against some Shredder Clones, the Foot Tech Ninja and the powerful Foot Mystics! As if that wasn't bad enough, Baxter Stockman decides now is the time to make his move...

With Stockman showing up in the middle of the final battle, our heroes must temporarily join forces with the Shredder to defeat his exo-suit before he annihilates them all. With everything working against them, high atop the Shredder's skyscraper, can our turtles emerge victorious?! And what roll does the Sword of Tengu have to play?

With Splinter mysteriously vanished, the Turtles are feeling frustrated, not knowing where to start looking. Impatient with strategizing, Raph heads off on his own - and straight into trouble, of the mobster kind!

As the Turtles continue their search for Splinter, they turn their attention to the Guardians. The trail soon leads them to a building marked as "TCRI" - the same letters on the canister of ooze responsible for their mutation! Now with two reasons to infiltrate that building, the Turtles recruit both April and Casey to help get them inside.

The Turtles successfully infiltrate the mysterious TCRI building, and locate the unconscious Splinter inside a stasis tank. But they also discover that there's more to the technicians inside then meets the eye...