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.

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. Now Splinter and April 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.

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.

Shredder completes the eye of Sarnoth, attaches it to his helmet, and plans to unleash its power on the world. However, when the Turtles intervene, the helmet falls into other hands.

Shredder & 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 Xenomorph-like creatures that hatch from the eggs in order to save the city.

Shredder gets Bebop and Rocksteady back as his henchmen in exchange for Baxter. When Krang tries to exterminate him, a freak accident occurs turning him into a mutant fly.

The turtles deal with four mutant frogs who are now under Shredder's command and also deal with a group of anti-mutant enforcers.

Donatello devises a cure to make Master Splinter human again. Meanwhile, Shredder plans to open a gate to Dimension X.

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

The Neutrinos return to Earth after hearing of Krang and Shredder's plan to get rid of the turtles via brain-drain. Shredder finds interest in their Starmobile's ability to open dimensional portals and tries to get his hands on it. Meanwhile, the turtles try to get the Starmobile's main energy source running again.

A freak accident from a transporter turns April into a cat-woman. Irma meets TMNT in order to rescue her.

While Splinter goes out on a retreat, the turtles must try to stop the Technodrome from returning to Earth.