For the next ten years, Jules served Robotnik as a mindless drone, his son Sonic believing him to be dead the whole time. After Robotnik's downfall, all Robians were freed from his influence and Jules and his wife Bernie re-emerged, aided by Uncle Chuck into reuniting with their son. When Robotnik's parallel-universe counterpart appeared on Mobius, he re-established control of the Robians, with the exception of Jules and Bernie who had been given magical Power Rings by Sonic as wedding bonds. The rings' power allowed the Hedgehogs to retain their free will, which they used to find out about Eggman's presence and sabotage his plans to conquer Mobius Prime. Jules broke cover as Eggman threatened to kill Sonic and with his help, the Freedom Fighters withdrew from Eggman's space station.
Roughly a year later, the aliens known as the Bem arrived in Mobius' orbit and abducted every roboticized Mobian on the planet. The Robians were returned the next day - completely restored to their original flesh and blood forms. All except for Jules, that is. As Sonic would discover when he met the Bem a year later, Jules remained a robot since he was mortally wounded at the time of his roboticization. If he was de-roboticized, his injuries would be re-opened and he would die.
Ever since the Sonic the Hedgehog comics' massive ret-con following the Sonic/Mega Man crossover Worlds Collide, Jules has been effectively erased from the comic's continuity and is unlikely to ever appear again.