After Shredder destroyed the world and murdered Splinter at the last season, the Turtles, April, and Casey Jones meet a new ally named Fugitoid. They decide to travel back in time to stop the Triceratons from collecting all the parts to the black hole generator. During the journey, they go through many strange worlds and struggle with lots of difficulties such as Lord Dregg, Overmind System, Krang and Kraang Subprime.