Devil's Due G.I. Joe vs Transformers continuity
Along with several other Transformers, the dormant Sideswipe was found on the crashed Ark by Cobra, who soon reprogrammed the alien robots to serve them. Sideswipe and Sunstreaker were rebuilt into Stingers and sent to assault the SPS Research Facility alongside Soundwave and his minions. The two brothers didn't succeed in their mission, though, as they were rammed aside by Wheeljack while charging at the building and were eventually ordered to retreat. Wheeljack later freed Sideswipe and the others from Cobra's control, and he helped Sunstreaker and Cliffjumper fight back against the similarly freed Decepticons and their former captors.
Two years later, Serpent O.R. took control of the Decepticon forces on Cybertron and captured Optimus Prime. Sideswipe joined a team of Autobots led by Hot Rod who were planning on charging in and rescuing their leader as soon as the opportunity came up. After reinforcements arrived in the form of G.I. Joe, the Autobots made their move and attacked Serpent O.R.'s Decepticon army, ultimately defeating it.
Sideswipe returned to Earth a few months later, where he worked to keep Cybertronian technology from being misused by humans. During one mission to Cuba, he helped stop Destro from selling S.N.A.K.E.s to one Mr. Calandero, but failed to capture the arms dealer and returned to the Autobots' base, the Arc II. When the ship was attacked by the Pretender Monsters, Sideswipe was the first to fall. The crew later received medical attention at the Pit, where they'd eventually recover from their injures.