In this version, Splinter and Casey Jones were already killed in battle, Michelangelo had lost an arm and Raphael lost an eye. Hun had Baxter Stockman's brain jar sewn into his right shoulder and was in a wheelchair with both of them now working with the rebels.
In a final battle with Shredder, the alternate versions of Leonardo, Raphael, Michelangelo, Hun, Stockman, and Karai died in battle, Donatello faced off the against Shredder himself, but the Shredder's massive exo-suit was too powerful for him to defeat head on. Don managed to kill the Shredder by shoving the Turtle Tunneler into his face. This left April O'Neil as the only surviving member of the main cast as she and the rebels worked to rebuild their world now that Ch'rell is dead.