On one normal night in New York city, 4 fully grown Mutant Turtles do their evening training with Master Splinter at their Sewer Den below New York. They've spent their 15 years with their sensei, Master Splinter and learning the arts of Ninjitsu. They've never reveal themselves to the outside world, due to their appearances. As it would lead them to trouble. But when all seems fair a pack of rubble eating tiny machines came into their Den and start chewing up the place. They battled these machines one by one with their Ninja skills. Unfortinately their den starts to collapse and they're'e now separated from their master. They contacted him by their own cell phones "Shell Cell" and they agree to meet up with him around the other side. But the way to the other side is blocked. So they'll have to go "top side" in other to get to the other side. And this will lead to battling one of New york's toughest gangs "The Purple Dragons".
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!
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.
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...
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.
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?
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 are taken across space to the Planet D'Hoonnib - and right into the middle of a Police arrest! They befriend Professor Honeycutt, alias The Fugitoid, who is being pursued by the military forces of General Blanque. The General wants Honeycutt's teleportation device, perhaps the only way The Turtles will reach Earth again...
Every three years, Splinter leaves his students to go to parts unknown. Curious, the four Turtles decide to follow him this time. The pursuit of their master leads the Turtles into something they never expected, right into the middle of the "Big Brawl" : The Battle for the Nexus, a brutal tournament where fates will be decided...
On Halloween night, a mustachioed man visits April, expressing interest in a rather unusual item: a hideous six-armed idol. But the statue is no ordinary junkshop knickknack; it can be used to invoke a horde of imps that proceed to clean out the city and bring its spoils to their master, a criminal who calls himself The King of Thieves.
The Purple Dragons have evolved from a basic street gang to a smuggling syndicate that works throughout New York. Leonardo goes with Casey to put an end to Hun's plans. However, Casey and the recently angry Leo will have to control their own fury if they want to bring justice-- and not just veangeance-- out of this.
The Turtles begin training with the mysterious Ninja Tribunal, experimenting with new powers and weapons. After securing the first of the Tribunal’s Lost Artifacts, our heroes learn to their horror that the “great evil” they are destined to face is the long-imprisoned spirit of the one, true Shredder!
The Turtles train with the Ninja Tribunal to prevent the resurrection of the Shredder. But when Splinter and the Ancient One express serious doubts about trusting the Tribunal, the Turtles are confused. If they all agree on the goal, why the doubts? To explain the danger to the Turtles, Splinter and the Ancient One reveal the secret history of the Tribunal… including the true origin of the Shredder!
The Turtles and company continue their training under the Ninja Tribunal, learning to fight in the physical as well as mental and spiritual worlds. They’re going to need that knowledge, because the second artefact of the Shredder has been found, guarded by a horde of nasty Tengu demons that eat Acolytes for breakfast… literally!
Returning to the Tribunal Monastery with the second Shredder Artefact, things seem to be going well for our heroes when – deception! Old foes infiltrate the Monastery. With all three artefacts in the hands of evil, they plan a sneak attack on the Tribunal and their students with devastating results!
The Justice Force is expanding its ranks, and Mikey plans on joining up as Turtle Titan!, while Leo is more concerned in alerting them to the threat of the original Shredder. But when Nano reappears (thanks to Bishop and Baxter Stockman), everything quickly spirals out of control into a super hero vs. nanotech slugfest! But has Nano come back as friend or foe? And will the Turtle Titan and Leo survive long enough to find out?
The original Shredder is resurrected by the Foot Mystics, whose first agenda is to destroy Karai – the “false Shredder.” And, while the Turtles are enemies of both Shredders, they realize that if the original Shredder wins, his goal of creating a world of destruction, devastation and chaos will be one huge step closer to reality. So, like it or not, they have to help Karai – even while she’s intent on killing them!
Weary after their first battle with the new Shredder, the Turtles doubt they can defeat him. To lift their spirits, Splinter and the Ancient One shares a tale of the Turtles’ toddler days. The story reveals that though the Turtles were small, they overcame impossible odds to defeat a phantom bent on reviving the Shredder, though they may not remember it.
The demonic Shredder has transformed New York City into a nightmare version of Feudal Japan and the rest of the world is next! But the Turtles have a plan, and if it takes allying themselves with some of their former enemies to bring the fight to the Shredder, so be it… because if they fail, there is no tomorrow!
The Turtles are shocked to find out one of their old foes from the past is still alive and well in the year 2105. Bishop has become a top agent in Earth's government, and even though he isn't after the Turtles, they don't trust him. But Bishop offers the Turtles an ultimatum if they wish to stop crime...
After an outing downtown, Mikey starts behaving strangely – as in super strength, green-slime-spewing strangely. The reason, the Turtles soon discover, is that Mikey has been “implanted” by one of Sh’Okanabo’s “gene-seeds”. Sh’Okanabo has begun his first test of introducing the seeds into the general population in order to propagate his alien race, transforming ordinary folks into monstrous Kanabo drones! But will our heroes be able to stop him before becoming “implanted” themselves?
Splinter announces that the Turtles will graduate to the next ninja rank, Chunin, for using the 3 pillars of life: being invisible, indestructible and showing insight. Except for Michelangelo, who skipped the exam to play video games. But Splinter gives him a last chance to graduate with his brothers.
An old enemy from the past returns, and he wants Bishop destroyed and only the Turtles can help him. However, when Bishop is kidnapped, the Turtles learn that before he became the Global President and cleaned up his act, he did some "dirty work" for the Earth Protection Force-- poaching and gene splicing aliens. It turns out that in 2055, there was a lab accident that had catastrophic results...
Torbin Zixx was selling disintegrator weapons to aliens and cheated Big Red out of merchandise. As payback Zixx promises him an experimental matter transmitter he doesn't have - but Boss Zuko does. Meanwhile, a meteor made of dark matter is on a collision course to Earth. Can the turtles get the transmitter from Zuko and stop the meteor? Or will Zixx get there first?
When the Time Window is finally repaired, the Turtles enter into it to head home, but instead of finding themselves back in the lair, our heroes find themselves with Viral! She’s escaped from inside Serling and has infected the Window so that she can send her most hated enemies on a harrowing, helter-skelter trip through the past, present and future and make them pay for all the pain they’ve caused her!
While Don focuses on collecting Splinter’s data bits, his brothers find themselves pulled into a war between The Foot and the Purple Dragons. But things get a lot worse when the cyber-Shredder finds a way out of the digital realm by taking over the powerful robotic body of his old crony, Baxter Stockman! With Splinter’s data bits just within his grasp, Don is forced to make a terrible choice, help his father or help save his brothers from the Shredder.
Serling, desperate to return to his own time, builds a makeshift Time Window. Unfortunately, he accidentally shrinks himself to five inches tall and goes on a time traveling adventure. Unfortunately, when he escapes the clutches of arguing Turtles, he is found by Wendell, an old man who has been hunting him since Serling destroyed his toy eighty years previously and wants to reproduce him.
The Cyber Shredder creates a web portal that he hopes will allow him to venture from cyberspace into the real world. The villain first tests the device by releasing all sorts of mutants and monsters from various online programs. The Turtles must take down the creatures before they tear the city apart… and shut down the web portal before Cyber Shredder is able to use it and enter into the real world!
During a night of showing off their extreme sports gear, the Turtles are attacked by a monster from beneath the Earth. They trace the beast to a remote island where they uncover their old foe, Dr. Baxter Stockman, who has created vicious monstrosities to unleash on the unsuspecting public. Starting March 7, 2009, a series of 13 shorts, called "chapters," ranging from 90 seconds to two minutes in length began airing on The CW4Kids during episodes of TMNT: Back to the Sewer and Chaotic: M'arrillian Invasion, as well as being streamed on the 4Kids website a week in advance of airing on television. They comprise a single story called "Mayhem from Mutant Island."[7] On March 27, 2010 the 13 shorts were re-aired edited together under just the "Mayhem from Mutant Island" title as a so called "new" episode of TMNT: Back to the Sewer.
The 2003 Ninja Turtles find their 1987 originals captured and held hostage by Hun. The 2003 Turtles defeat Hun, and the Purple Dragons and rescue their classic originals and escape to the modern Turtles' Lair. Meanwhile, the Technodrome from the 1987 TV series along with Shredder, Krang, Bebop and Rocksteady are together again and fight both versions of the turtles. Meanwhile the classic Shredder, transports the Utrom Shredder back from the ice asteroid that he was sent to after the "Exodus" episode. The classic Shredder and Krang had no idea that the modern Shredder would turn against them and sets out to erase the entire Ninja Turtle Universe, starting all the way back to the 1984 Mirage Comic series to where the Ninja Turtles are as of today, including the 1987 TV series Turtles, the live-action turtles, all the comic book turtles, and the modern TV series Turtles.