When his employee April O'Neil discovered his plans, he sent the Mousers after her, saying that she knows too much. With the help of the TMNT, she escaped and returned to Stocktronics Corporation to defeat him. The Turtles and April finally corner Stockman, who calls his Mousers, and retreats. As the building went down, Stockman was taken by Hun to see Shredder. The price for his failure was his left eye which Hun removed.
Stockman would then use the information he got from studying anUtrom exosuit the Foot found to create the invisible Foot Tech Ninjas, in an attempt to defeat the Turtles. Stockman later captures Raphael, with the help of "Foot Tech Ninjas." Hun interrogates Raphael, but allows him to escape to allow Foot Tech Ninjas to follow Raphael back to the Turtles' lair.
The Turtles successfully fend off the cloaked ninjas, with Donnie's heat-sensing goggles. When that plan failed he was carried off by the Foot Tech Ninja, Stockman was injured by Hun to the point that he was in a wheelchair with a neck brace and missing his right hand, which is replaced with a robotic prosthesis. Stockman is in a severely debilitated state at this point, but he still works for the Shredder hoping to gain access to the Utrom exosuit.
When the Shredder had his vengeance against the Turtles (Shredder Strikes Back arc), he wanted proof positive that the Turtles had perished. He sent Baxter to get proof that the Turtles died but threatens Stockman with a "final punishment" if he doesn't come back with conclusive evidence. Stockman performs a survey of the antique store, but finds no human or mutant DNA.
Distraught at this finding, Stockman made his own proof and gave it to Oroku Saki in exchange for the Utrom exosuit to study. Convinced that the Turtles are dead, Saki gives him access to the exosuit.
Having been subjected to harsh punishment by the Shredder on more than one occasion, Stockman quickly develops an animosity for the Shredder and Hun. With newfound and unfettered access to the Utrom exosuit, he plans to use the suit to create something that will give him more power. When the TMNT returned to New York and took revenge on the Utrom Shredder, he uses the surprise attack by the Turtles as an opportunity to launch his own plan of revenge against the Utrom Shredder.
Stockman would bust in, using a giant four-armed robot to try to get revenge on all 5 and Hun. Stockman attacks the Shredder's throne room and battles the Utrom Shredder, Hun and the Turtles. The Turtles and Shredder had to temporarily work together to defeat the mad scientist. Despite being a near indomitable foe, Stockman is defeated and seemingly explodes in the night sky.
Later, Stockman would be reduced to a head on a spider robot body that was voice activated by Saki. He is controlled remotely by the Shredder with a robot eye implant that covers up his previous wound that shocks Stockman when he disobeys his orders or becomes arrogant. Using him to sneak inside the T.C.R.I. building, the secret hideaway of the Utroms, the Shredder would have Stockman tamper with the virtual reality program the Utroms were using to explain their origins to the Turtles, so that if they died in VR, they would die for real.
Stockman shuts down the security of the base, and leads the Shredder and his men to an underground path that allows them to enter the building unseen. Once the TMNT broke free, Donatello had Fugitoid an ally of the Turtles imitate Shredder's voice to release Baxter from his control. Now free, Stockman attacked the warlord, whom he still holds a grudge against, and in part contributes to the Shredder's defeat and everyone would discover that he was actually an Utrom. After this incident, Stockman escapes and disappears.
With the Shredder's defeat, Stockman would set his head in an Utrom Exosuit chest cavity, protected by a glass jar and first try to trick Leatherhead for his own evil schemes. Working independently, Stockman befriends Leatherhead and helps the crocodile build a transmat device in exchange for help with his robotic body, and the Turtlebot, a robot created to fight the Turtles. Stockman's Robot is completed but Stockman's ruse is revealed when Leatherhead finds out that the scientist used to work for the Shredder. Stockman's Turtlebot is destroyed, but he escapes. By this time, Stockman no longer has the financial backing and material support of the Foot.
Later with his head now on the shoulders of the Utrom exo-suitwork and the chest cavity covered up, he worked with the mob in an attempt to rid the city of the Foot and the Purple Dragons, and win the gang war. With the Shredder gone, a turf war developed, and Stockman creates robots to get rid of the Foot and the Purple Dragons. Stockman's robots are destroyed and he survives the turf war.
Hun would somehow find Stockman again and reduce him to just a brain connected to an eyeball and spinal column in a stasis tube, and once again put him under the Shredder's command. Ch'rell did quote upon seeing Stockman's current appearance that he "should've quit while he was a head." The tank housing his brain allows him to speak, hear, and communicate with other foot techs, but it is also equipped a volume button, and electrical shocking device, which Hun and the Shredder use to torture the scientist.
This form of coercion was used to get Stockman to create a group of Foot Mechs (robotic soldiers). The Foot Mechs are eventually destroyed along with the Utrom Shredder's Freighter Headquarters. Stockman's tank rises from the water after Karai rescues the Shredder before sinking to the bottom of the ocean.
He is eventually fished out the water and continues to work under the Foot. Still a brain in a tank, Stockman has upgrades added to his tank, which include a modified self-propulsion system, a crude robotic arm, and a 360° hologram of his head. Despite an enmity shared between Stockman and the Shredder and the likelihood that Stockman will turn on him, Ch'rell keeps him around because he considers him to be useful.
This attitude begins to change when, because of Stockman's failed attempts, a new scientist named Dr. Chaplin was introduced, Chaplin considers Stockman to be a role model and would build Stockman a new robot body that would project a hologram image of his head. While Chaplin admired his work and looked up to him, Stockman was always trying to get rid of him due to threats by Ch'rell about making Chaplin a permanent replacement as the new head engineer of the Foot.
Stockman even goes as far as sabotaging Chaplin's inventions so that the younger scientist's success would not negatively affect him. Not one for gratitude, Stockman continues to plot against Chaplin, but his attempts backfire and only boost the junior scientist's worth in Ch'rell's eyes. Stockman's tries to sabotage Hun's mission to rescue Karai in Hun on the Run, but he soon becomes a contact within the Foot for Agent Bishop.
Eventually, Stockman would double cross the Shredder one last time. A significant act of sabotage is seen when Stockman places a program that locks the controls of Ch'rell's starship in "Exodus, Part 1." When the ship is finally destroyed, and believing his enemies to have perished, he now worked alongside Bishop and joined the Earth Protection Force in exchange for a new body.
For the time being, Stockman upgraded his robotic body with four legs and four arms. Despite being an expert in robotics and engineering, Bishop changes Stockman's role and has him create clone aliens controlled by remote control in Aliens Among Us. The genetic material from these aliens inadvertently leads to a mutant outbreak. Stockman, who had been promised the tools he would need to create a new human body, is told that he is unable work on his new body until the outbreak is neutralized. Stockman is then sent to New York in "Outbreak" to contain the threat.
Despite working with EPF forces to contain the outbreak, Stockman is unsuccessful. Although Stockman is told that he is unable to work on his body, he divides his time between creating a new body and the outbreak. Bishop warns Stockman that he should not go through with the process, given the outbreak he caused. Stockman disregards Bishop's warnings goes through with a cerebral transfer into his new human body in "Insane in the Membrane."
Stockman finally made a new human body for himself but in his impatience, his work was rushed. Once his consciousness had been transplanted, the new body seems fine at first. But it decayed rapidly and in his desperation to halt the process, Stockman ended up losing his mind, which leads to the scientist having visions of his mother.
In his insanity, he decided that all of this had begun when April sent the Turtles after him, so he sought to destroy her. Stockman heads on a lone mission to seek revenge on April. In the end, Stockman's delusions of his mother made him save his former assistant instead, and he apparently fell to his death into the East River. Not being done with Stockman's work, however, Bishop found and revived his brain.
Bishop has Stockman's body recovered and his brain placed in a new cyborg body. However, when the scientist is brought back to life, he is mortified that he wasn't left to rest in peace. Under Bishop, Stockman is forced to work on a cure for the outbreak. He never figures out the cure as Leatherhead discovers it in "Good Genes ".
After the outbreak is neutralized, Stockman and Bishop inadvertently destroy the Heart of Tengu, an artifact that used to control the Foot Mystics. This act sets off a chain of events leading to the return of the original Shredder.
In an alternate future, where Ch'rell ruled Earth, Stockman's brain was attached to an aged, wheelchair-bound Hun. They worked with Donatello (who had been stranded in this dystopia by the Ultimate Ninja and Drako), the Turtles resident in that alternate reality, and April in an attempt to overthrow the Shredder. When they went to face him for the final showdown, Hun begged Ch'rell to take him back. Ch'rell, now using a giant-sized exosuit, stomped both Stockman and Hun flat.
Stockman reappears in the fifth, "Lost" season of the series, still under Earth Protection Force employ. During his first appearance of the season, in the episode "Membership Drive," Stockman has programmed his cyborg body to reflect a hologram of his human body over him. He attempts to reprogram the reactivated Nano (found during a fortuitous E.P.F. salvage operation), with disastrous results (When Nano escaped, Bishop commented that he was beginning to understand why his former employee kept relieving him of body parts). Later, in the two-part season finale, he forms part of the turtles' offensive against a resurrected demon Shredder. In these episodes. he has a tank-like body. At the end of the final Lost Episode, his robot body was almost completely destroyed in the final battle with the Tengu Shredder's dragon form and what was left of it was carried away by Bishop's soldiers with his holographic head saying resignedly "It seems the pain will never end."
- In the episode What a Croc! Baxter Stockman gets a new body in this episode. His head is now attached to an Utrom exoskeleton.
- A Better Mousetrap
- Attack of the Mousers
- The Way of Invisibility
- Tales of Leo
- Return to New York, Part 1
- Return to New York, Part 2
- Return to New York, Part 3
- Secret Origins, Part 1
- Secret Origins, Part 2
- Secret Origins, Part 3
- What a Croc!
- City at War, Part 1
- City at War, Part 2
- City at War, Part 3
- Rogue in the House, Part 1
- Rogue in the House, Part 2
- Nobody's Fool
- New Blood
- Mission of Gravity
- Hun on the Run
- Same As It Never Was
- Exodus, Part 1
- Exodus, Part 2
- Dragon's Brew
- Bad Day
- Aliens Among Us
- Insane in the Membrane
- Adventures in Turtle Sitting
- Good Genes, Part 1
- Good Genes, Part 2
- Membership Drive
- Enter the Dragons, Part 1
- Enter the Dragons, Part 2
- Head of State
- Hacking Stockman
- Mayhem from Mutant Island