Shredder returns from Dimension X. However, Krang says until Shredder proves himself trustworthy cause he failed to defeat the turtles and Splinter with Krang's technology, he will be denied the aid of his Foot Soldiers or Rocksteady and Bebop, who are still stuck in Dimension X. Shredder goes to a corrupt, sleazy karate school and teaches the students how to commit crimes while dressed as the Turtles in an attempt to discredit the real Turtles. Shredder also frees Baxter Stockman from custody a
The turtles seek out the fragments of the eye of Sarnoth, a crystal with unimaginable power. After finding the first fragment, Shredder steals it and uses it to shrink the turtles. Shredder also tries to convince Krang but Krang insists Shredder that he will only believe it if he brings the turtles on a plate for Krang. Now Splinter and April O'Neil must intervene. April is able to enlarge the Turtles, but our heroes lose in the end as Shredder escapes with the first fragment.
After discovering that a mutant plant has had its growth accelerated by the first fragment of the Eye of Sarnoth, Shredder unleashes it on the city to attack the Turtles. Meanwhile, April is lured into a trap by Shredder, and is immediately captured. However, the Turtles disguise themselves as pizza delivery boys and free her, though Shredder escapes, again, with the fragment, while the Turtles must destroy the mutant plant that is wreaking havoc on the city.
Upon finding the second fragment of the Eye of Sarnoth, Shredder uses it as a power source for a supercomputer named Omnis, in the hopes of opening a portal to Dimension X. Meanwhile, the Turtles must deal with machines that suddenly go haywire all over the city.
The Triceratons do battle with the General Blanque's forces and in the chaos, allow the Turtles to capture the Triceraton Prime Leader as their hostage. They prepare to return home using the Fugitoid's teleporter, but there's only one problem : he's never tested it
Krang sends the eggs of Xenomorph-like creatures, which look like meatballs, in order to assassinate the Turtles. Baxter Stockman then rigs a contest so that he and Shredder can deliver the deadly pizzas to the Turtles. However, due to heavy customer demands the Turtles end up getting ordinary pizzas, and the booby-trapped pizzas are out somewhere in New York! Shredder and Baxter may have ended up becoming victims of their own plots when the pizza monsters do not discriminate between ally and en
Tired of Baxter Stockman's constant failures, Shredder sends him to Dimension X in exchange for bringing Bebop and Rocksteady back to Earth as his henchmen. When Krang, unable to find any more use for Baxter, tries to disintegrate him, a malfunction causes Baxter to instead cross-mutate into a fly. * This episode was created as a tribute to the classic 1958 science-fiction horror film The Fly. Its 1986 remake film of the same name premiered one year before the series began.
Shredder is running low on mutagen, so Krang sends a canister that ends up in the Everglades due to transdimensional problems. Shredder sees the mutagen canister broke, but did create four mutant frogs whom he befriends and gets to commit robberies, as well as to hate the Turtles. Donatello realizes Shredder is ordering robberies of chemicals in order to mass produce mutagen. The Turtles must not only face the misguided Frogs, but their job is complicated due to the NYPD now having an anti-Turtl
The Turtles retreat to Casey Jone's Grandmother's farm house to reflect on their recent battles. But the figure of the Shredder still haunts their every memory. What is the Shredder's connection to the Turtles origins?
The Ultimate Ninja, a warrior from across the galaxies, has come to take the head of Shredder - only to find Leonardo has already done the deed. So now The Ultimate Ninja challenges Leonardo in a battle to the death...
The Neutrinos return to Earth after hearing in on the plan of Krang and Shredder to get rid of the turtles via brain-drain. Shredder finds interest in their Starmobile's ability to open dimension portals and tries to get his hands on it, and meanwhile the turtles try to get the Starmobile's main energy source running again.
The Turtles are about to discover that the Mutagen that transformed them, has had an effect on other creatures as well. They must now defend their territory from the rampage of the insidious alligator Leatherhead...
The Turtles return to the underground city but they find the city is now abandoned, it's crystal moon power source missing, and it's human population reduced to monsters. Can an unstable serum created by Donatello restore the humans to normal?
The collapse of Shredder's crime empire means the city is open for the most vicious gangs to seize control for themselves. New York is plunged into chaos and anarchy, and only the Turtles can maintain order..or can they?
The Turtles are caught in a power struggle for the city : The Foot, the Purple Dragons, and the Mob, all want a piece of the pie. Are the boys able to save the city from anarchy? And is it their problem in the first place?
With the Foot, the Purple Dragons, and the Mob becoming more than the Turtles can handle, the TMNT reluctantly call on the help of Shredder's old General: Karai.
Whilst testing out their new Shell Sub, the Turtles are forced to sink or swim when they discover their old enemy Garbageman is creating his own underwater city.
Casey Jones joins the sport of Super Slam Hockey. However it turns personal when a legendary 17th century Golden Puck is taken by crooks. Can the Turtles hold Casey in line long enough to find the Puck, or will the hardcore rules of Super Slam Hockey get to them first?
Shredder deploys an army of Foot Mechs and a Cyborg duplicate of Splinter against the Turtles.
Shredder's army of Foot Mechs confront the Turtles, but even if they defeat this army, can they stop Shredder? And how does a Triceraton warrior called Zog fit into it all?
The Turtles help April unlock the secrets of an ancient Puzzle cube left behind by her father. The puzzle's solution takes April and the Turtles on a journey of discovery..to another dimension filled with giant insects!
Michelangelo's quest to collect a rare comic take the TMNT and Casey Jones back to Northampton, Massachusetts. Here they uncover a plot by a madman to kidnap the members of a retired super-hero team called The Justice Force.
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...
The Turtles discover more about their master Splinter as the Battle Nexus tournament continues. They also have a run-in with a warrior who Splinter defeated in the tournament three years ago: Lord Draco.
The Battle Nexus tournament begins to take it's toll on the TMNT : Leonardo is poisoned, Splinter is framed, and Lord Draco moves closer to victory.
The Battle Nexus Tournament nears it's conclusion : Dontello finds himself fighting for his life with Usagi Yujumbo as Mikey is poised to become Battle Nexus Champion. Leonardo's condition worsens, and Splinter is still in prison. Worse still, Lord Draco now has control of the Daimyo Warstaff...