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This question is a little out-of-universe, but it's got me curious.

In Attack of the Clones, we see the massive clone army that Palpatine has secretly arranged for the Republic. These clones are assigned to and fight alongside the Jedi until, in Revenge of the Sith, Palpatine tells them to "Execute Order 66" which means to kill the Jedi.

I could be wrong about this, but I don't believe that it was until season 5 of the Clone Wars TV show that the issue of inhibitor chips were brought up. The chip malfunctions and causes a clone to kill a Jedi far too soon, causing Fives to go searching for an answer. He discovers that they were all made with chips in their heads that would cause them to lose control and kill the Jedi.

This element of the chips is brought up in Rebels and TCW season 7, but was it always supposed to be this way? Was the original plan in Revenge of the Sith that the clones were being mind-controlled? Or was that a later element from TCW to give a reason for why the clones would turn on their Jedi?

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In Legends the clones had free will, because they weren't brainwashed but indoctrinated. (take the people of North Korea as a real life example, they have free will seeing they aren't mind controlled but they are thought to obey and don't know how not to.)

From birth they were trained to be one cohesive unit and fully dependent on a command structure. So if a higher ranking officer gave them an order, they followed it. But they were able to think negatively of the order but they were so indoctrinated that they just followed orders due to them not realizing they had the choice to disobey.

This is why Palpatine actually made the Jedi's Generals during the clone wars, because simply said the Jedi were arrogant and were terrible at leading armies. The bad choices of many Jedi to lead to a large number of pointless casualties. And mistakes aside the Jedi were more then willing to sacrifice clone lives seeing they were considered less seeing they were not part of the natural order of the force. Because of these character flaws and lack of military experience the clones started to resent them and were more eager to execute their orders(and the jedi).

in Dark Lord: The Rise of Darth Vader - Part II: The Emperor's Emissary Vader is even tasked to hunt down Clones that disobeyed. In it Palpatine says:

Contagion brought about by fighting alongside the Jedi for so many years. Clone or otherwise, there is only so much a being can be programmed to do. Sooner or later even a lowly trooper will become the sum of his experiences.

This was especially true amongst the Arc-Troopers and Clone commando's who were less heavily indoctrinated so they can function more independently when cut off from the command structure.

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The only pre-TCW source I've found for Order 66 being involuntary is the non-canon Tag and Bink: Revenge of the Clone Menace (2006). In this comic, reacting to the words "Order 66" by trying to kill Jedi is apparently a genetic condition inherited from Jango Fett, who attacks the titular Tag and Bink after the 66th order is called in Dex's Diner:

Panel from Tag and Bink showing Jango Fett in a diner saying "I've got this sudden urge to kill Jedi, and I kinda like it!" while shooting at Tag and Bink. Dexter Jettster blocks a shot with a spatula and says "Run for it, boys!"

That said, this comic is a humorous "what if" story and wasn't considered canon even at the time.

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