Some TMNT stuff really isn't for little kids.
As a young boy, Baxter's father Robert Stockman taught him how to play chess as a method of honing his skills, intelligence, and tactical abilities. Baxter, in turn, later used these attributes to take StockGen away from his father.
He would later do business with the mysterious warlord General Krang, who provided him with the resources to create a supersoldier mutagen, a psychotropic compound to enhance intelligence, and natural body armor based on turtle shells. However, these projects attracted the attention of Shredder, due to the intervention of one of Stockman's employees. Much to Stockman's dismay, both the mutagen and the psychotropic compound were stolen and lost.
Over the next several months, Baxter would use the mutated alley cat Old Hob to hunt the former lab rat Splinter, in hopes of reclaiming an untainted sample of the psychotropic compound. His relationship with Krang also became strained, as Baxter had failed to complete two of the three scientific projects he had been contracted for.
He eventually allowed Old Hob to use his robots, nicknamed M,O.U.S.E.R.S., to capture Splinter. While Splinter was soon lost to StockGen for the second time, Baxter's technical skills impressed Krang. Baxter was drugged and transported to Burnow Island, where he found that Krang was an extra-dimensional Utrom who wished to use his engineering abilities to complete a terraforming fortress known as the Technodrome.
During his time working on the Technodrome, Baxter attempted to undermine Krang by installing malware in the computer systems, and even attempting to kill the Utroms in cryostasis. He formed an uneasy alliance with Zayton Honeycutt, but the robot scientist turned against him when he learned that Baxter planned to take control of the Technodrome as a weapon. Baxter interfered with Honeycutt and the Turtles' attempts to stop him by unleashing an army of M.O.U.S.E.R.S., but Krang easily dispensed with his malware. Defeated, Baxter used flyborgs to flee the Technodrome.
Upon his escape from the island, Baxter used flyborgs to rescue the suffocating Shredder, and proposed a mutually beneficial partnership, showing Shredder his new headquarters at T.C.R.I. At Shredder's behest, he began using flyborgs and M.O.U.S.E.R.S. to hunt down Splinter, but his creations were destroyed by a squad of Foot Ninja led by Karai. When Splinter challenged Shredder to the Gauntlet, a disgusted Baxter left the Foot headquarters.
Sometime later, he was confronted by April O'Neil, and was shocked to discover that she knew all about his prior dealings with Krang and Shredder. However, before he could respond to this revelation, the building was invaded by the mutant scorpion Zodi and a small army of Darkwater mercenaries, forcing Baxter to ally himself with the Turtles in order to survive. After the conflict concluded, he reluctantly took April as his new partner.
He found himself working with them again when the Turtles needed to be teleported into the Pantheon's family reunion, which he only did with the promise of financial gain. During the invasion by the Triceratons, Baxter benefited from the crisis by selling essential supplies to citizens who were trapped in their homes. He played an important role in the invasion's conclusion, using a teleporter to transport all the Triceratons on Earth to Burnow Island. Due to the intervention of Elizabeth O'Neil, he was able to take full credit for stopping the invasion single-handedly. However, immediately after a press conference, he was taken by Detective Kara Lewis to see Agent Bishop, who obtained the current location of the Triceratons from him.
April continued advising Stockman in how to further enhance his image in the city, suggesting that he could use his MOUSERs to deal with the burgeoning rat problem, while knowing that the Rat King was causing trouble. He agreed, and the unleashing of his robots helped the Turtles to triumph over the Rat King, as well as unearthing the presence of Leatherhead. He then publicly declared his candidacy for the office of New York's mayor, a goal which he later achieves.