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.

After re-energizing the present-day Turtles, the Turtles of the past have only 3 hours to get back to their time, or they will all cease to exist. Meanwhile, during the 15 hours it took to re-energize the Turtles, the remainder of Dregg's invasion fleet has been completed and has been unleashed on the city and now the Turtles and Carter have to stop Dregg, Krang, and Shredder.