The very first Star Wars movie makes it clear that most of the Jedi were wiped out by the evil Galactic Empire, and fans spent decades wondering exactly how those without the Force could overpower and kill those with the Force as their ally. When Revenge of the Sith came out, we saw how simple it was: Emperor Palpatine executed Order 66, causing Clone Troopers across the galaxy to murder the Jedi near them, often by shooting them in the back or simply overwhelming them.
But if you’ve ever wanted the dirty details of Palpatine’s scheme, we’re here to explain everything you need to know about Order 66.
Each clone had special behavioral modification biochips inside their brains that could make them extremely hostile to Jedi at a moment’s notice.
When Revenge of the Sith first came out, it wasn’t clear exactly how Order 66 was orchestrated. Palpatine simply gave the order and loyal clones like Commander Cody were suddenly willing to kill their Jedi allies like Obi-Wan Kenobi. At the time, the most popular theory was that this was some kind of hypnotic command that the clones were bred to respond to if they heard the order.
However, The Clone Wars show made it clear that there was a mechanical component to Order 66.
Specifically, each clone had special behavioral modification biochips inside their brains that could make them extremely hostile to Jedi at a moment’s notice. There were certain dangers to this approach: on at least one occasion, a clone’s chip malfunctioned, and he had to be killed in order to preserve the secrets of Palpatine’s plotting.
Did the Clone Developers Know About Order 66?
Another question Star Wars fans had when Revenge of the Sith came out is whether the otherwise peaceful Kamonioan cloners knew all the details about Order 66 or not. The answer is yes and no: they obviously knew about the brain chips because they were the ones who installed them, and they generally knew the chips could instill hostility towards Jedi.
However, they were led to believe this would only be if the clones needed to hunt and kill rogue Jedi, and they had no idea that Palpatine was plotting a massacre on a galactic scale.
Once Palpatine initiated Order 66, the effects were instantaneous. As we saw in Revenge of the Sith, Clone Troopers throughout the galaxy betrayed and murdered the Jedi they were serving. Some Jedi and former Jedi like Ahsoka Tano managed to survive, though, and she helped to remove the chip from Rex’s brain, rendering the fan-favorite clone friendly to her yet again.
As for the Jedi who survived Order 66, almost all of them went into exile afterward. In the Original Trilogy, we see that Obi-Wan Kenobi and Yoda each settled on remote worlds. This was mostly true of fellow survivors like Quinlan Vos, who later ended up helping smuggle other surviving Jedi to safety.
Not all Jedi who survived Order 66 were as lucky as Obi-Wan, Yoda, and Vos, though. For example, Jedi Master Luminara Unduli survived the initial attack only to be taken prisoner by the Galactic Empire. She was eventually executed by the Empire, which held onto her remains in order to more authentically bait a trap for future Jedi.
Some stronger-willed clones were able to overcome their programming, and many more began to question the Jedi-killing order that had literally been implanted in their brains.
While Order 66 mostly had an effect on its Jedi targets, it also continued to have an effect on the Clone Troopers via the chips in their brains.
For example, most of the Bad Batch was immune to the effects of the chips, deserting the Empire and later having their chips removed by Rex. And some stronger-willed clones were able to overcome their programming, and many more began to question the Jedi-killing order that had literally been implanted in their brains.
Interestingly, the effects of the brain implants began to wear off over time, implying that Order 66 was meant to be fully executed in a very short period of time. However, Palpatine also knew that the service of the clones was temporary, and in The Bad Batch, we see the cloning facility destroyed and the official Imperial transition between Clone Troopers to Stormtroopers.
Brain chips were no longer needed: Imperial propaganda ensured that everyone from soldiers to citizens thought of the Jedi as a myth, and Palpatine’s Inquisitors would quietly hunt the remaining Jedi until they were disbanded shortly before A New Hope.