So no, not all clones follower order 66, and its my thinking that Rex was more in touch with his human traits as apposed to his clone traits. Boba Fett had some old clones in his camp, and its then he laerns how he can stop the age advance. Later in the Jedi series ( then one where Jacen goes sith ) its learned that some clones went to mandalore and set up camp there with some jedi survivers. In the Clone Wars series it does mention some clones not following order 66, fiver being one of them, and a bunch of them then set out to help outher clones escape.
It's just that Order 66 inherently labels Jedi as traitors and that, the clones being the good soldiers they are, it was carried it out to the letter with thoughts of betrayal on the mind. It was to my knowledge that Order 66 wasn't so much "hardwired" but drilled into their minds just like any Article or General Order of the Sentry in actual militaries. Order 66: "In the event of Jedi officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander (Chancellor), GAR commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established." The orders are flash memory added to them in their "childhood" and are contingency in-case of coup, like for example Order 65: "In the event of either (i) a majority in the Senate declaring the Supreme Commander (Chancellor) to be unfit to issue orders, or (ii) the Security Council declaring him or her to be unfit to issue orders, and an authenticated order being received by the GAR, commanders shall be authorized to detain the Supreme Commander, with lethal force if necessary, and command of the GAR shall fall to the acting Chancellor until a successor is appointed or alternative authority identified as outlined in Section 6 (iv)." They must protect the republic, so most of the normal clones obey it without any issues, the thing is if High command tell them the Jedi are attempting a coup they dont have time to go check if its true, orders are orders, most normal clones obeyed but some with more independent and better view of the Jedi (like a few commandos and "Sons" of Skirata) didnt go through with the plan.
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