In the series, Stockman explained that he always had an evil streak in his heart as a child prodigy being pushed around by his classmates, so he decided to make himself an amazing intellect by presenting a volcano with real lava at the school science fair. To his dismay, however, that resulted with the entire gym burning down and him getting expelled. As an adult, he tried re-developing his intellect by getting a job as an inventor at TCRI, but was fired for an incident involving spilled copier toner, so he vowed revenge on his classmates and co-workers for making a mockery of him and his failing intellect.
He first appeared in "I Think His Name Was Baxter Stockman," where he was seen trying to break into a building in a shriveled suit of armor. The Turtles stopped him, but Stockman came into possession of Donatello's T-Pod (which has a military-grade artificial intelligence chip) and incorporated it into his armor. This results with the armor upgrading itself into a larger size, proving him a competent threat to the Turtles, who still expressed sympathy for the hapless scientist. During "Mousers Attack," he was shown to have created the Mousers to steal electronics from underground. But when they interfered with the Foot Clan's new plan to kill the Turtles, he was captured by Dogpound and brought before Shredder, who forced him to join the Foot Clan, believing his genius to be a useful asset. However, by "Baxter's Gambit," Stockman became tired of being regularly harassed and threatened by Dogpound and Fishface, so he sought to eliminate all of his enemies at once, and trapped the two with the Turtles in a deadly maze. He was defeated when the two groups unexpectedly joined forces against him, and he fled the Foot Clan.
In "Mikey Gets Shellacne," Stockman was revealed to have secured a large amount of mutagen, seeking to create an army of mutants to serve him. Unfortunately, he was sought out by Karai to be taken back into the Foot Clan when cornered by Dogpound, who he claimed he can return to his human form. As a precautionary measure, Dogpound placed a collar containing mutagen around Stockman's neck, vowing to mutate him if he double-crossed him. After Dogpound was mutated into Rahzar and the villains were defeated by the Turtles, Stockman was brought back into the Foot Clan once again, with a collar containing a set of miniature mutagen vials locked around his neck, which was meant to mutate him if he attempted another betrayal.
In "The Lonely Mutation of Baxter Stockman," Shredder became weary of Stockman's poor progress in making effective mutant warriors and activated the mutagen collar on him. As the result of a housefly landing on his nose before the collar exploded, Stockman mutated into a humanoid mutant housefly with a lobster-like black claw for a right hand, a vertical mouth releasing an acid that dissolves metal, heightened hearing and superhuman flight speed that dubbed himself Stockman-Fly. Though he was a far more competent threat in this mutated form, Stockman's attempt to secure retro-mutagen from the Turtles failed. Taken before the Shredder, he pledged complete loyalty to the Foot Clan, believing them to be his best chance at returning to his human form.
In "Legend of the Kuro Kabuto," Stockman participated in the massive hunt to retrieve Shredder's stolen helmet. During the fight with Turtles over it, he accidentally kicked Fishface, who then called him Buzzkill, which Michelangelo remarked as what he should have dubbed the mutated Stockman. In "Vengeance is Mine," he created a batch of mutagen meant to mutate the Turtles into serpents and mindlessly eat Splinter, though that did not go as the Shredder planned because Karai (who was being used as the bait) got mutated instead, and the following fight ended up destroying his lab.
Several 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".
- Baxter Stockman managed to hack into your T-Phone signal.
- Shredder's threat to remove Stockman's legs may be a nod to his first punishment of the scientist's failure back in the 2003 series.