What happened to the clones who fought along side the sith and who fought along the jedi. This is a star wars theory post. This is what I think happened to the clones who fought alongside totally diffrent people. This is what I think happens to clones after the Republic, the clones who tried to protect the jedi by taking out their chip probally got killed except captain rex,and commander wolfe. Commander Cody and Comander Gree became Generals in the empire and trained the new generation of clones in the empires academy.Since clones get older 2 times as much as regular humans,or aliens.So I think the Empire genrals passed before the blow up of death star and ithink the ”traders”to the empire are going to die in the star wars rebels thanks for reading!Go to my youtube channel Ill post my account in one of my next posts.