- Shredder - Stockman was spared by Shredder after his M.O.U.S.E.R.S interfered with Shredder's feud against the Turtles, mainly because he found his talented inventing skills very useful to his clan, which led to several improvements, such as making Fishface a pair of robotic legs, thus making the latter a more powerful combatant. Shredder, however, for the most part, cares little for Stockman and he probably chose to dislike him even more after the scientist trapped Dogpound and Fishface in the "Maze of Doom". Fortunately, Shredder's favor is still bought back by Stockman through the creation of a formidable or even decent mutant army Stockman makes for him.
- Dogpound / Rahzar - Stockman was found useful by Dogpound because he is an inventor who was capable of hacking into April's phone (which contained information on Splinter's whereabouts). Despite being allies, Dogpound and Fishface harassed Stockman when he wouldn't follow their orders. As a result, Stockman betrayed them by trapping them with the Turtles in his Maze of Doom. Although Stockman escaped after his defeat, Dogpound crossed paths with him sometime later and asked Stockman to help him become human again, which failed when Dogpound mutated into Rahzar. So in order to ensure that Stockman kept his promise, Rahzar outfitted him with a mutagen collar that would warn him not to attempt another betrayal.
- Fishface - Stockman was viewed by Fishface as an ally at first, because he was capable made a pair of robotic legs and a water-breathing rig for Fishface, but when he and Dogpound harassed him when Stockman wouldn't follow their orders, he betrayed them by trapping them with the Turtles in his Maze of Doom. Even though he escaped after his defeat, Fishface crossed paths with Stockman again and asked him to help him and Rahzar to become human again, outfitting him with a mutagen collar to ensure that Stockman kept his promise.
- Tiger Claw - Stockman-Fly is often got in touch with Tiger Claw, if for any assignment Shredder has Stockman-Fly do or if how any new mutant creations are coming along.
- Bebop - Stockman-Fly was made a fool of Bebop when he threw a flash bang at him and sending him crashing into a billboard, so Stockman-Fly probably dislikes him for it, despite fixing his cloaking technology.
- Leonardo- Stockman's name is tended to be forgotten by Leo (examples: "Dexter Backsman", "Daxter Boxman", "Blister Speckboy", etc.)
- Raphael- Stockman and Raph interacted very little, even when Raph got pleasure by throwin him in the trash.
- Michelangelo- Stockman unintentionally got the T-Pod from Mikey, and he used it upgrade his armor and make him a more dangerous villain. After Mikey put bees onto his face, Stockman's dislike for the Turtles increased.
April O'Neil- Stockman-Fly kidnapped April and planned to use her as a backup plan for the hope of Donnie giving him the retromutagen, which is to merge with her through mutagen and become one. However, because of her Kraang DNA, April is immune to the mutagen.
Casey Jones- Stockman-Fly encounters Casey when the teenage vigilante, Donnie and Leo came to stop him from dropping April into his mutagen tank. Afterwards, Casey rides with April on her dad's back and helps them keep Stockman-Fly from getting his hands on Donnie's retromutagen.
- Pigeon Pete- Stockman-Fly and Pete don't interact much. During the battle in Shredder's lair, they fight by slapping each other,