While the Turtles work on using fragments of the Vortex Crystal to stabilize their mutations, Lord Dregg plans to use the fragments to create another Vortex Crystal to power his Vortex Transporter. Meanwhile, Dregg's second-in-command, HiTech, is blasted into space, to be replaced by Dregg's top scientist, Mung, as his new second-in-command.

Lord Dregg teleports Shredder and Krang from Dimension X to the Dreadnaught in order to learn more about the Turtles and Earth's weapons. Meanwhile, after permanently stabilizing his mutation, Carter finally leaves the Turtles and returns to college.