Order 66had arguably its best retcon inStar Wars: The Clone Wars, yet its added context to the devasting directive was what George Lucas had in mind forStar Wars: Episode III - Revenge of the Sith. Order 66 initiated theJedi Purgeand, tragically, was the true purpose of the Clone Army, whose clone troopers fought alongside the Jedi throughout the three-year Clone Wars. Considering how often clone troopers and officers befriended their Jedi leaders, it could be difficult to believe that they would betray them immediately upon receiving Order 66.
In both the originalStar WarsLegends continuitydepictions and their modern canon iterations seen in properties likeThe Clone Wars,clone troopers of all ranks and typesare demonstrably good men with free will. Order 66 completely changed this, compelling them to kill all Jedi and turn on the democratic ideals they otherwise fought and died for.The Clone Warsand other properties revealed that the clones were brainwashed to follow Order 66, making their abrupt betrayal make far more sense.

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George Lucas Always Planned Order 66 To Be A “Manchurian Candidate Concept”
The Clone Warsseason 6’s Order 66 story arc established that all clones had inhibitor chips implanted in their brains since embryonic development. Once Order 66 was issued, clones lost their free will, followed the directive, and became loyal minions of the fledglingGalactic Empire. While this might seem like a massive retcon for the order, it owes its origins to George Lucas’s ideas forRevenge of the Sith. In a 2014 interview withIGN,The Clone Warsshowrunner Dave Filoni notes:
From my earliest conversations with George coming onto Clone Wars, as far back as 2005 when I put to him “What was Order 66, and how did it work?”, he was always connected to the idea that it was somewhat of a Manchurian Candidate concept. When the order goes down, it’s not like the clones have a real way to say, “No, I’m not going to do this.”

Clone troopers being brainwashed to follow Order 66 did not originate in the modernStar Warscanon, however.Properties from the original Legends continuity noted that clone troopers were indoctrinated to follow the order, but the method of brainwashing was not specified. Moreover, Legends-era ARC troopers were mostly unmodified, resulting in instances of ARCs simply refusing to follow Order 66. As shown in modern canon properties, like Greg Weisman’sStar Wars: Kanan: The Last PadawanandStar Wars: The Bad Batch, many clone troopers overcame the effects of their inhibitor chips after Order 66.
In the original Legends continuity, Order 66 was one of the Clone Army’s 150 contingency orders. In the modern canon, Order 66 was kept secret.

Clone Wars Fulfilled George Lucas' Vision Better Than Revenge Of The Sith
The Order 66 retcons inThe Clone Warsand Legends-era properties were necessary, asRevenge of the Sithdid not convey that the clone troopers were brainwashed to follow the order. The film makes it appear as though the clones were mostly willing participants in the Jedi Purge. Clone Wars-era materials from both continuities did the necessary work of confirming that clone troopers would not kill the Jedi nor fight for a totalitarian regime in their right minds - thoughThe Clone Warsno doubt did the best job of it.
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