[@Shiny Keldeo] I could see his commander letting him go but escaping with a fleet is highly unlikely. Perhaps a squad or two or ARC troopers at most, as the Biochip's would have the other clone's attacking even if their commander tried to stop them. Officers were often normal people, many of whom owed loyalty to the Chancellor not the Jedi and would believe him first.

I'm fine with him being a Jedi and such, perhaps he simply escaped with the ARC's and then took them to the Rebel Alliance allowing ARC troopers to pass their training on to the Rebel soldiers? I don't want anyone having backing fleet's or anything. Your Jedi and his Padawan are welcome to join. As most Clone troopers of the first batch are dead by this point.