Three months later, in "Return to New York," Stockman-Fly was provided with a new lab guarded by a trio of crustacean-like mutant clones of Shredder and new supply of mutagen. In "Serpent Hunt," he used this mutagen supply to assist Shredder with the mutations of Bebop and Rocksteady. He would oversee the Shredder's ongoing project to develop a serum that would grant the Shredder control over the subject's mind, as seen in "Casey Jones Vs. the Underworld", "The Noxious Avenger", and "Clash of the Mutanimals." After making a cameo as the referee of Fishface's underground race in "Meet Mondo Gecko", Stockman succeeds in returning Karai to a human form by the time of "The Deadly Venom", having perfected the mind control serum worms. Stockman would later hack into the Turtles' T-phones and loan Karai his Mousers during her gambit to kill Splinter in "The Fourfold Trap". Stockman also participated in the fight against the Triceratons but as Shredder kills Splinter the Earth is condemned to be destroyed and frightened Stockman is absorbed by the Black Hole in "Annihilation: Earth! Part 2", but a new version of him is created alongside a new timeline when the Turtles save Earth from the Triceratons in "Earth's Last Stand".