Summary Palpatine designed Order 66 as a trap for the Jedi, using inhibitor chips implanted in clone troopers to strip them of free will by activating genetic coding. The clones who resisted Order 66 were more individualistic, explaining why Captain Rex could resist killing Ahsoka Tano. Order 66 was heartbreaking for the clones, who were forced to murder their Jedi friends, and Palpatine ultimately replaced them.
Star Wars has finally explained how Order 66 really worked – and why some of the clone troopers were able to resist it. Palpatine designed the Clone Wars as the ultimate Jedi trap, because the Jedi lost as soon as they chose to wage war in the first place. But Order 66 was Palpatine’s ultimate triumph, as – all over the galaxy – the clone troopers turned on the Jedi Generals who had commanded them. Star Wars: The Clone Wars explained why even heroic clones had gunned the Jedi down, revealing all the clones created by the Kaminoans had been implanted with inhibitor chips that stripped them of free will.

Lucasfilm has finally revealed just why the inhibitor chips were so effective, and why some clones were able to resist Order 66. The Lucasfilm Publishing Panel at San Diego Comic Con 2023 released images from the upcoming Star Wars book Dawn of Rebellion: The Visual Guide, and the text reveals the true nature of Order 66 – and why Palpatine was so disturbed when some clones resisted it.

“The secret weapon of the Order 66 command, encoded into each clone’s genetic make-up, needed complete, uniform subservience to work. When the time came, the order’s execution largely succeeded, but there were a few strong-minded clones who resisted.”

Order 66, it seems, was encoded on a genetic level. The more individualistic a clone became, though, the more they resisted it; this explains why Captain Rex managed to resist killing Ahsoka Tano in Star Wars: The Clone Wars season 7.

Related: Star Wars: Every Jedi Who Survived Order 66 (In Canon)

Star Wars Has Completed Its Order 66 Retcons

There is a sense in which the various Order 66 retcons have gone full circle. The inhibitor chips were introduced in Star Wars: The Clone Wars in part to fix a narrative problem; George Lucas and Dave Filoni wanted viewers to genuinely care about the clone troopers, even though everyone had already seen Star Wars: Episode III – Revenge of the Sith. But, as the stories continued, Lucasfilm couldn’t resist showing some clones who resisted Order 66 – including Clone Force 99 in Star Wars: The Bad Batch. This latest reveal finally pulls all the threads together, explaining why most of those mutant clones weren’t effected by Order 66.

Order 66 is truly heart-breaking for the clones. Most had come to care a great deal about their Jedi Generals, and they were effectively forced to murder their friends. Worse still, the effect of Order 66 faded with time, leaving the clones confused about what was going on. Palpatine, meanwhile, was concerned at the individuality some clones had shown, and decided to replace the clones. They ultimately became yet more victims of Star Wars’ greatest villain.

Source: Lucasfilm