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.
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 & 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.
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.