In the final season, set a year after the fifth season, Stockman is not shown to be explicitly working with Bishop, instead offering his services to his old ally and enemy Hun. New York City is at war again, this time between the Foot and the Purple Dragons; Hun and Stockman are on the side of the latter. However, the Cyber Shredder hacks into Stockman's robotic body, mind-controlling him and eventually forcing him into an alliance with the Turtles to evict the Shredder from his body. In his final appearance in the series, Stockman clones an army of mutant dinosaurs to wreak havoc on New York for no apparent reason, but the Turtles stop him and turn the dinosaurs docile.