Shredder returns from Dimension X and sets out to frame the turtles with a group of thugs dressed as them while Dr. Baxter Stockman uses the Ultimate Rat Catcher on Master Splinter.

While practicing their martial arts in Central Park the Turtles witness an alien spaceship crash into a small pond. They dive in and rescue the pilot, he warns them that they must find the 'Three Fragments of the Eye of Zarnof'. The alien tells the Turtles that when the three pieces are joined together, they will bestow power unknown to any earthling. He gives them a Crystal Converger to help them locate the Three Fragments before they fall into the wrong hands.

Shredder sheepishly reports to Krang that he has lost the First Fragment and needs Krang's help. Krang agrees and, with his hi-tech equipment, locates the Fragment just outside the city near where a traveling carnival show has pitched their tents. Meanwhile, the Crystal Converger has led the Turtles and April to the same carnival. Before they can locate the Fragment, it is found by two small boys.

After the batteries died in the alien crystal converger, Donatello, using spared circuits from the space ship, builds a tracking device to help locate the second fragment of the Eye of Zarnov. On the streets, the tracking device picks up the signal and leads the Turtles to a branch of a bank where a hold-up has just occurred.

The Turtles are still on the search for the last fragment but Shredder beats them to it. Connecting all three to his helmet he creates a deadly weapon to battle the turtles. The helmet changes hands several times from the battle but eventually finds its way back to Shredder. He uses the helmet to create an army of giant golems at the San Francisco bridge. The Turtles discover that the fragments are becoming dangerously unstable, and they race to tell the villain to rid himself of the eye before it explodes!

Shredder and Baxter Stockman switch meatballs on some pizzas, used as prizes in a contest, with some weird alien eggs from Dimension X. The Turtles must battle the creatures that hatch from the eggs in order to save the city.

Shredder attempts to use the world trade center in an experiment, but the failure of Baxter's essential new device, plus the interference of those heroes in a half shell, prevent the villain's plot from succeeding. Frustrated at Baxter's latest failure, Shredder contacts Krang in Dimension X and demands that Rocksteady and Bebop be sent to aid him. Krang informs shredder that an exchange must be made to enable the portal to open properly, Shredder has the perfect candidate to take Rocksteady and Bepop's place: BAXTER! So, with a quick gesture (literally, Shredder actually throws Baxter into the portal), the transfer is made, and Shredder gets his old henchmen back. Baxter's fate, sadly, is not so pleasant, Krang immediately orders his execution, and he is sent to the disintegration chamber. A tiny Fly is his sole company inside the chamber as the device is activated. But fate has other ideas for the scientist.

Shredder's latest scheme is to acquire more mutagen and create more mutants but, due to an ion storm in Dimension X interfering with the dimensional portal, Krang is forced to transport the mutagen canister 'blind-folded', it lands in a Florida swamp rather than the Big Apple. Shredder heads south to recover the canister and discovers four mutant frogs. He realizes their potential and makes plans to return to New York City with them.

Sensing Master Splinter's despair at his new life as a rat, the Turtles agree to use the small amount of mutagen that they have left to concoct a formula that will revert Splinter back into Yoshi. The experiment is a success and Yoshi decides to take a stroll, as a human, through the city. Meanwhile, April is reporting Public Service Announcements from the local library when spies Rocksteady and Bebop. She immediately contacts the Turtles who head straight for the library where they encounter Shredder. It seems that Shredder has stumbled onto a spell that will enable him to open a portal to any dimension he chooses.The Turtles find a reference to a temple in an old subway terminal somewhere under the city.

A robot cop, Rex-1, helps April and the Turtles defeat an evil army of robot cops under the control of Shredder.

While cruising around Dimension X, the Nutrinos decide to 'buzz' the Technodrome. However, when they fly by, they notice that a cargo bay door is open and can't resist the temptation. Inside, they tap into a transmission between Krang and Shredder on Earth. Through this transmission, the Nutrinos learn of Krang/Shredder's latest plan to destroy the Turtles. The Nutrinos decide that they can't sit idly by and watch, so they open their own portal and arrive on Earth to warn the Turtles.

While experimenting with a Matter Transporter in his secret hideout, Shredder sends Rocksteady and Bebop to a nearby garbage dump. Through a series of mishaps, Rocksteady and Bebop find themselves in the sewers and in the Turtles' Lair. The Turtles contact April O'Neil and lure her with the promise of a great news story, but when she arrives she discovers that they need a new TV to replace the one that Rocksteady and Bebop destroyed during their encounter. It seems the 'boys in green' are addicted to sci-fi movies and were in the middle of a marathon when Rocksteady and Bebop dropped in.

Krang, sick of Shredder's constant failings, makes a shocking resolve to return the Technodrome to Earth. Krang sends Shredder an energy-converter from Dimension X and instructs the villain to take over the hydroelectric station at Niagara Falls.