Actually, not all the clones and clone commanders followed Order 66.
Read Dark Lord: the Rise of Darth Vader. According to that book while
most of the clones turned on their Jedi commanders many had become
loyal to their Jedi commanders and refused to turn. That allowed a
handful such as Olee Starstone to escape alive and go into hiding. Of
course, Darth Vader then hunted them down and killed many of them the
point I'm making is that according to the books not all the clones
were totally loyal to Palpatine. Although, most of them were..

On 5/7/11, Clement Chou <chou.clem...@gmail.com> wrote:
> 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.

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