Actually, the empire and republic are considered two completely different entities... because of how the system was run. The clones were programmed to obey whoever was in charge of the empire as that plan was apparently in place long before the clones were thouht of as a military resource. This is shown in Revenge of the Sith when Palpatine issues "order 66" and the clone commander responds, "It will be done, my lord." At least to me, this implies that the knowledge of who they're working for has already been programmed into their subconscious and was waiting for that trigger. Until then they were all-too-happy to serve the republic and obey the Jedi, since many of the squads have Jedi leading them. For anyone who doesn't know about order 66... this was the order to begin the "jedi perge." All the clone commanders turned on the Jedi who were leading them, including Obi Wan... who was the only one who managed to escape from them. Well, there are a couple more I can think of, but the empire eventually caught up with them.. and the Jedi perge was also happening on Coruscant, as Anakin Skywalker, who was by then known as Darth Vader, had already turned to the Dark Side and personally slaughtered all the Jedi in the Temple.

At 09:39 AM 07/05/2011, you wrote:
Well...that's a bit confusing. The way I understood it they were programmed,
as such, to obey the Republic. COnsidering that the empire was the republic,
they had to obey.

Best Regards,

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