Star Wars: The Clone Wars featured a slight retcon to Order 66, making it the clone troopers' worst nightmare. When Order 66 was first shown in Star Wars: Episode III - Revenge of the Sith, little was known about it other than that the event was planned by Emperor Palpatine. The clone troopers that were primarily underutilized in the Star Wars prequel films swiftly turned into enemies of the Jedi, with the movie portraying the clones as more black-and-white traitors.
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However, upon the release of the animated series Star Wars: The Clone Wars, more depth began being attributed to the clones. From exploring their individual personalities to their bond with each other and the Jedi, the clones became worthwhile characters in their own right, making Order 66 much more tragic in retrospect. Similarly, SThe Clone Wars featured another clone retcon in the form of Order 66 and the inhibitor chips, with this story arc making the fateful Jedi Purge the greatest nightmare of the clone troopers in heartbreaking fashion.
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Clone Wars Season 6 Hinted The Clones Were Subconsciously Aware Of Order 66
One of the best arcs in all of Star Wars: The Clone Wars comes in season 6 in the form of Fives' Order 66 arc. Fives was a clone ARC trooper who discovered the inhibitor chips that would force the clones to destroy the Jedi when ordered, yet tragically ended with Fives' death before he could reveal this information to the Jedi. The arc begins with a clone trooper named Tup whose inhibitor chip malfunctions, forcing him to kill a Jedi before Order 66 is enacted.
Upon his death, Tup refers to Order 66 as "The mission... the one in our dreams." Tup then says that he is finally free of the nightmare before dying. This makes it clear that the clones were always aware of Order 66, if only subconsciously. Without knowing what it truly meant, the clones always knew that Order 66 was a part of their creation and that it was always going to happen, yet could not do anything to stop it.
Order 66 Was The Day The Clones' Nightmare Became Real
This retcon of Order 66 only made the event more tragic than it already was. In proving that the clones always feared Order 66 - referring to it as a nightmare - Star Wars made the day the Purge took place more heartbreaking. The day Order 66 was enacted was the day that the clones' nightmare became real. At the time, many clones did not see it this way, due to the inhibitor chip forcing their hand in destroying the Jedi. However, Star Wars has made it clear when focusing on the clones after Order 66 that they slowly regretted their actions after their nightmares came to .
The Clones Always Lived In The Shadow Of Order 66
These explorations of the clones after Order 66 prove that the fear they shared regarding the nightmare was warranted. The clones never truly escaped the shadow of Order 66, no matter how many defied the Order or the Empire after it rose to power. This has been explored more recently in Star Wars: The Bad Batch. Clone Force 99, due to their unique creation, did not suffer the effects of the inhibitor chip, besides Crosshair. Despite this, the Jedi failed to trust them, and they were forced to flee from the Empire with the galaxy seeing them as traitors.
The exploration of Crosshair and other clones that served the Empire in The Bad Batch also proves how the clones continued to live in the shadow of Order 66. Crosshair's arc saw him eventually resent the Empire, with the clones being seen as nothing more than tools to enact the Empire's will - like they were with Order 66. Other clones, like Commander Cody, eventually abandoned the Empire after being guilt-ridden over their actions during Order 66, proving they cannot escape the fateful day.
Another arc during The Bad Batch centers on the replacement of clones with stormtroopers by the Empire. One of the biggest reasons for this comes from iral Rampart and the clones destroying Kamino on the orders of Palpatine. When this is exposed, Palpatine pins the blame solely on Rampart and uses the clones' "blind" loyalty to push the conscription of stormtroopers. As the galaxy sees the clones as blindly loyal to anyone, especially after the events of Order 66, Palpatine succeeds, truly proving the clones never escaped the horror of Order 66 even after Star Wars: The Clone Wars.