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Baxter Stockman was trying to break in the copy store that he was fired from, wearing a homemade battle suit. It was implied that his employment was terminated for breaking a copy machine. The turtles noticed this and overwhelmed him. Stockman ended up getting shoved in a dumpster. After the turtles left, Michelangelo accidentally dropped the homemade MP3 player (dubbed the "tPod") created by Donatello. Stockman noticed this and the tPod upgraded his armor to great power levels. His armor became bigger and fully powerful and terrorized the copy store.
His name was revealed when one of his former coworkers recognized his face. The turtles encountered Stockman, but they were totally overwhelmed with his upgraded battle suit. After the turtles were defeated, he shoved all of them into a dumpster. Soon, the tPod merged with his armor, and he became even more powerful. Michelangelo named this version of Stockman the "Stockmanpod." He began to rampage through New York. The turtles ended up fighting the Stockmanpod on top of a building. Once again, Stockman was overwhelming the turtles.
He asked them if they had any last words. To which Leonardo responded by saying "bees," then Michelangelo shoved a beehive right on Stockman's face, using Splinter's philosophy about defeating armored foes. The confusion caused his suit to reveal the tPod and fall off the roof. Leo then destroyed the tPod, making the battle suit useless. Stockman got out of the suit and asked if they can call this a tie. Raphael responded by throwing him in a dumpster and saying "now it's a tie."
In Mousers Attack, Stockman created his Mousers to steal and attack. He sprayed Leonardo and Raphael with a gas that has the Mousers tracking them down no matter where they go. Then, Stockman gets captured by the Purple Dragons and gets taken to Dogpound. He lets him go when he tells him that they have a common enemy in the turtles. Bradford then has Stockman attempting to hack into April O'Neil's stolen phone. The turtles destroy April's phone, and Stockman tries to spray the turtles with the Mouser tracking gas, but Donatello throws a shuriken on the spray can, getting Stockman and Bradford sprayed with the gas instead, causing the Mousers to attack them. Stockman has been taken to the Shredder for interfering with his plans. He contemplated killing him, but decided that he can be of use to him due to his technical expertise.
In Baxter's Gambit, Stockman was tired of being abused by Dogpound and Fishface and set up an elaborate labyrinthine trap for them and the turtles. The turtles and the villains had to work together to avoid lasers, spiked balls, and fans to get to Stockman. When they finally got to him, he had a giant robot waiting to destroy them all. After getting the robot under Stockman's platform, Raphael and Fishface did a double team move to destroy the robot with that platform. But the evil engineer escaped with his helicopter helmet.
In Mikey Gets Shellacne, Stockman soon sets up a headquarters in the battered remains of TCRI, so he can start creating his army of Mutants. The Turtles find him there while looking for a molecular centrifuge. As Stockman unleashes the M.O.U.S.E.R.S. to attack the turtles, Dogpound also arrives. Dogpound manages to get his hands on both Stockman and the molecular centrifuge. Upon Dogpound seeing some mutagen tanks in Stockman's lab, the deranged engineer states that he has been planning to make an army of mutants. When Stockman claims that he can make Dogpound and Fishface humans again, Dogpound places a mutagen collar around Stockman's neck as "insurance," however the turtles and Dogpound battle, eventually resulting in Dogpound falling ,into one of Stockman's mutagen tanks, and mutating into Rahzar, who proves to be incredibly powerful in combat. However, Stockman's project is crashed by Michelangelo, when the latter tricks Rahzar into striking an electric power plug. Stockman, Rahzar, and Fishface are all shocked when the sprinklers are activated by Donatello. By the time Stockman wakes up, the turtles are gone and Karai has arrived at his lab, where she tells him that he is going to work for her and the Shredder again.
Stockman then makes a few minor appearances throughout The Manhattan Project, Part 1, mostly while talking to Rahzar and Fishface.
In The Lonely Mutation of Baxter Stockman, Stockman is first seen in his lab, working on his computer. The Shredder enters with Rahzar and threatens Stockman after his various attempts at making a mutant army for the Foot failed miserably. Before leaving, the Shredder activates Stockman's mutagen collar, covering him in mutagen and transforming him into a fly-human hybrid after a fly lands on his nose. Some time later, the now-mutated Stockman is wandering around his lab, now depressed that he will never be taken seriously as an engineer. He then comes to the conclusion that combining his mutated DNA with pure human DNA will result in a being more powerful than he was originally. Rahzar then enters the lab with two Foot-Bots, curious about what Stockman mutated into. Stockman, under cover of darkness, destroys the Foot-Bots and covers Rahzar in stomach acid before flying out a window. Later on, as he searches for a human to combine his DNA with, he overhears the Turtles attempting to use the newly made Retro-Mutagen on Kirby O'Neil, and attempts to steal it for himself. This results in the destruction of the first dose before it can be used. Returning to his original plan, Stockman grabs April and brings her to his lab. He ties her up above his vat of mutagen and explains his plan to her. Casey Jones, Leonardo and Donatello then arrive to save April and fight off Stockman. During this fight, it is revealed that April is immune to mutagen, explaining why her DNA worked as the catalyst for the Retro-Mutagen. Rahzar then breaks in with several Foot-Bots, wanting the Retro-Mutagen for himself. Donatello, April, Leonardo and Casey escape with the Retro-Mutagen, and Stockman and Rahzar follow. This results in a large-scale chase involving the Turtles, Stockman, Rahzar, several flying Foot-Bots, and Casey and April riding on Kirby's back. In the end, the second and final dose of Retro-Mutagen is nearly destroyed, but April manages to cover Kirby with it, returning him to normal. Later on, Stockman is dragged into the Shredder's lair by several Foot-Bots, and is ordered by Shredder to make one last mutant for him, or have his wings plucked.
In The Legend of the Kuro Kabuto, Stockman is one of the individuals sent out to retrieve the Shredder's helmet. He is paired with Fishface.
In Vengeance is Mine, it is revealed that the Shredder had Stockman working on a special kind of mutagen, which would turn the turtles into mindless snakes upon exposure. Stockman does not let the Shredder know that he accidentally spilled in an extra chemical during the creation of the mutagen, and states that everything is ready. The Shredder uses Karai as bait, setting her up to be mutated but not planning on letting her fall in. However, when the turtles and Splinter come to rescue her, she falls in and gets mutated anyway, setting fire to Stockman's lab in the process.
In Return to New York, Stockman has gotten a new lab, with a giant vat of mutagen, and the Shredder Elite as personal body guards. Before being assigned to cure Splinter's amnesia, he is seen working on retro mutagen. The turtles arrive in his lab to release Splinter, and Stockman attempts to call the Foot for support, but fails to do so. Outnumbered, he "evens the odds" by releasing the Shredder Elite to back him up. This appears to work until Splinter's amnesia is cured, at which point he destroys the Elite. By this point, however, Mikey has inadvertently called the Foot to the lab, and the turtles leave with Splinter.
In Serpent Hunt, Stockman appears at the end of the episode. His only significant role in this episode is mutating Ivan Steranko and Anton Zeck into Rocksteady and Bebop.
In The Pig and The Rhino, Stockman is seen alongside the Shredder and his other mutant henchmen who watch Steranko and Zeck become enraged after helping his master mutate them at the end in the previous episode. They prepare to fight the two mutants who try to attack the Shredder, but they are told by the Foot leader to stand down for he will deal with them himself. He then watches the Shredder easily dodge their attacks and defeat them. He then watches his master offer them a deal to serve him to which they both agree to. He then orders them to find and capture Karai like they did before and not to fail for the consequences will be severe.
In Casey Jones VS. The Underworld, Stockman is seen in his lab where the Shredder is as he checks Karai who is being held in a small glassed in habitat. The Shredder then commands him to find a solution to turn Karai back to human and soon. When the Purple Dragons arrive and give the Shredder more of the chemicals he is looking for, Stockman states that he does not have the necessary equipment for the chemicals. The Shredder angrily demands that he find the equipment, which he agrees to.
In The Noxious Avenger, Shredder sent Bebop and Rocksteady to obtain ingredients for him to complete his mind control serum. He is seen later on working presumably on the mind control serum.
In Clash of the Mutanimals, Stockman infects Slash, Dr. Tyler Rockwell, and Raphael with mind-controlling worms. Later, when the other Turtles and Mutanimals break into the Shredder's hideout, Stockman engages in a fight with Pigeon Pete.
In Meet Mondo Gecko, Baxter appears as a referee for Xever's race against the captured Michelangelo and Casey Jones as well as Mondo Gecko. He later spectates the match, accidentally regurgitating on Tiger Claw's food.
In The Deadly Venom, Baxter finishes synthesizing the Mind Control Serum to be much more lethal before administering a brain worm into Karai, who is now capable of retaining intelligence in mutant form according to Stockman through unknown methods.
In City at War, Baxter is at an injured Shredder's bedside in the Foot Clan's new lair and is injecting Shredder with mutagen.
He is Shown later in The Insecta Trifecta, with Tiger Claw and his other henchmen having become useless as of late, Shredder finds it ironic that he's turning to Stockman for help due to how loyal he has been helping the Shredder with his recovery, reminding him that the mutagen drip he administered to help Shredder recover is a batch designed to avoid the side-effects of normal mutagen. Bolstered by that show of faith in him from Shredder, Stockman begins his plans to reimburse the Shredder's money caches with creating two new mutants to help him, Antrax and Scumbug, also mentioning how with his new bug henchmen, he'll have friends to have around whenever he's not serving the Shredder. Their first target is robbing a bank, where they are confronted by two officers from the NYPD. Scumbug easily overpowers both of the officers, while Stockman tempts Antrax with candy to get him to rob the bank. When confronted by Casey and Raphael, Raphael leaves Casey to fend for himself as his bug phobia causes him to run away in fear. Casey is captured, and at his new lair, Stockman is warned by Scumbug that the Turtles will probably find them soon enough. Realizing he's right, Stockman plans to move to a new hideout in a skyscraper construction site, but first decides to go after Karai for all the trouble she's caused to the Shredder's criminal empire. Attacking her at Shredder's old lair, Stockman is able to capture her, only for the rest of the Turtles to intervene, but thanks to Raphael suffering another panic attack, Stockman kidnaps not only Karai, but April and Leonardo as well. Taking them back to his latest lair, Stockman plans on using his prisoners as food for his bug henchmen, before the other Turtles attack the hideout, and thanks to Raphael using a mantra taught to him by Splinter, he's able to overcome his bug phobia to defeat Stockman, rescue Leo and the others, and force Stockman to abandon his henchmen and flee back to the Shredder in defeat. Though Stockman prepares to face the consequences as he reports his mission a failure to Shredder, Shredder is not concerned in the slightest as he points out to Stockman that his mutagen drip he administered to Shredder is finally taking effect as Shredder begins to mutate as razor-sharp blades emerge from his arm and the back of his hand.
In The Super Shredder, Stockman comes to see if Shredder is fine. However even he's receiving the mutagen drip. Shredder desires his strength back as fast as possible so he orders Stockman to give him the rest of the mutagen. Stockman refuses since the formula is too unstable and would cause disasterous results to Shredder's sanity. Threatened being ripped apart until his head, Stockman agrees and then the unstable mutagen kicks on Shredder, turning him into a super mutant. Tiger Claw comes to see what happened and blames Stockman for what happened to Shredder but his master says its what he desired and refuses to let Stockman finish the dozes, saying its time to prepare a trap for Splinter. He watches Splinter, The Turtles and April approaching to the part of the sewers Shredder fought Splinter making Michelangelo having the strange feeling there being watched.
Like his early counterparts in the comic franchise and the 2003 cartoon series, Baxter Stockman is an African American man. He has round glasses, an afro, and wears a wool sweater and jeans. His physical appearance is close to the comic version. After being mutated, his appearance is similar to that of a common house fly, with multiple eyes, wings, a retractable mouth and a left arm that is similar to a fly's leg. He still has his human legs and his normal clothes, however, for some reason, his right hand is a giant lobster claw like appendage, even though it should be just like his other arm.
Baxter Stockman's rather timid and dorky appearance belies a vicious and vengeful heart. He harbors deep rooted resentment at a world that he feels has constantly wronged him. In Baxter's Gambit, he admitted that he was "full on mega crazy." Stockman is looked down upon by other people as a weak, pathetic person, which only adds more fuel to his resentment, although he often acts as just that when facing dominating personalities, such as Rahzar or the Shredder. The main thing that can make Stockman surprisingly dangerous is his skills in engineering powerful weapons, robotics and various other useful inventions; though he has a rather humorous habit of incorporating the phrase 'of doom' into their names. After he was mutated, his sanity seemed to degrade further as he became much more aggressive and sadistic, showing a particular joy in mutating, or attempting to mutate, others into monsters. Stockman also seems to have become more willingly servile and attends to the Shredder's demands gleefully instead of fearfully. Perhaps most notable of all is his new sweet tooth, much like real flies, and it seems a chocolate bar is enough to buy his loyalty. Stockman is also shown to value friendship and loyalty to Shredder above all else, as both of these values resulted in the creation of Scumbug and Antrax, the only friends he ever had, although he ended up abandoning them in order to make sure Shredder had someone to check on him, a decision that genuinely hurt him.