For years, Charles was forced to serve Robotnik as an obedient worker-bot, performing manual labour or supervising various facilities in Robotropolis. All the while, he was aware of his actions but was unable to control himself, his mind supressed by Robotnik's programming. However, during a failed experiment conducted by Robotnik and Snively, Charles was freed from Robotnik's control and from then on helped Sonic and the Freedom Fighters by acting as a spy for them. This would last until Robotnik discovered Chuck's betrayal during Project: Endgame.
After Robotnik's death, Chuck assisted in recovering Mobotropolis by acting as a peacemaker between his fellow Robians and angry Mobians who were embittered by their roboticized kins actions while under Robotnik's influence. He would also reunite his nephew Sonic with his parents, Jules and Bernadette. The fragile peace would be completely shattered when a parallel version of Robotnik appeared on Mobius to take his Prime counterpart's place, and his first act was to send out a control signal to all the roboticized people on Mobius, brainwashing them and using them to re-establish control of the old Robotnik's territories. Sir Charles was among the unfortunate Robian masses and became Eggman's lieutenant for a time after the doctor re-conquered Robotropolis. Thanks to Sonic and the magical Sword of Acorns, Charles would be again freed from Robotnik's control.
In the comic's 123rd issue, the aliens known as the Bem blanketed Mobius with a de-robotization field, reverting all Robians across the planet (except for Jules Hedgehog) back to their original flesh and blood bodies. Since being de-roboticized, Sir Charles has gone from being Knothole's chief scientist to a member of New Mobotropolis's leading council.