As Baxter Stockman and Bolivar Trask unleash the sentinels, The entire X-Men are kidnapped and held hostage, and are planned to be killed in 72 hours. But only Wolverine and a group of four new recruits are able to escape and flee into the sewers, where they are met by four turtles, whose master was also abducted by robots made by Stockman. Now they have to save the X-Men and Master Splinter and also defeat The Foot Clan, who have been backing both Trask and Stockman.