Following the stories from the 1987 cartoon, Baxter Stockman would again try to sell off his Mousers to a pest control agency, and be thrown into the street. Shredder would use his Mousers to try to get rid of the Turtles and Splinter. The Turtles would tie up Baxter and interrogate him and leave him there to be taken away by police. Later, he'd be in an insane asylum where Shredder would again use him for his evil plans. However the Archie Comics would make a radical retcon and u-turn of events during their take on the Eye of Sarnath arc. Here Shredder and Baxter managed to only find the first half of the crystal. While Shredder and Baxter were running from the Turtles, Armaggon, a mutant shark from the future, appeared and grabbed Shredder, offering safety in exchange for help against the Turtles. We assume this only left poor Baxter alone to face the Turtles and the police.
In the first 3-issue arc (based on the first 5 TMNT episodes), Baxter's hair was colored white for some reason, though he was again blonde in the regular series(He also strangely had shorter hair in the first two issues of the ongoing series). He is never mutated into a fly, and after the first issues he is only seen in the short flackback in the Future Shark trilogy.