Here Is Why Clones Betrayed the Jedi & Switched Sides

order 66

When we saw the events of ‘Star Wars Episode III: Revenge of the Sith,’ we saw that Supreme Chancellor Palpatine initiated what he called “Order 66” right after defeating and killing Mace Windu. This order compelled all of the clone troopers, who had spent the last three years fighting alongside the Jedi, to kill all of them on sight and without hesitation. As such, the clones betrayed the Jedi and contributed to the destruction of the entire Jedi Order. So, why did the clones betray the Jedi?

The clones were created to have inhibitor chips inside their heads. These chips compelled them to blindly follow certain orders that could only be initiated by none other than Supreme Chancellor Palpatine. As such, as Order 66 was initiated, the clones could not control themselves when they shot the Jedi.

Back when ‘Revenge of the Sith’ was released, some fans thought that the clones were just too obedient and were meant to follow any of Palpatine’s orders without question. But thanks to the events of ‘Star Wars: The Clone Wars,’ we got to know more about the clones who were given personalities in that series. Now, let’s look at why or how the clones betrayed the Jedi.

Why did the clones blindly follow Order 66?

Introduced during the events of ‘Star Wars Episode II: Attack of the Clones,’ the clone army that was created using the genetics of Jango Fett was commissioned by the late Jedi Master Sifo Dyas to provide the Galactic Republic ca grand army. Of course, while the Jedi Council saw the clones as sketchy at best, the Republic still used them in the war against the Separatists because they had no option. The Jedi Order would not be enough to defeat the army of battle droids that the Separatists had, and that’s why the clone troopers were essential to the Republic.

Then, during the events of ‘Star Wars Episode III: Revenge of the Sith,’ which took place three years after ‘Attack of the Clones,’ the Clone Wars was already on its final legs as Count Dooku had been killed. The death of General Grievous spelled the end of the Clone Wars, as Mace Windu and a few other Jedi Masters were on their way to Supreme Chancellor Palpatine’s office to make him give up his emergency powers. Of course, Anakin had previously informed Windu that Palpatine could be the Sith Lord they had been searching for the entire time.

Of course, many things happened in that scene in Palpatine’s office. But the Supreme Chancellor defeated and killed Mace Windu with Anakin’s intervention. Skywalker turned to the dark side and became Darth Vader. And after that, Palpatine called Commander Cody, who was on Utapau, to initiate Order 66.

order 66

Utapau was where Obi-Wan Kenobi was sent to defeat General Grievous. Without hesitation, Commander Cody ordered a canon to shoot at Kenobi, seemingly killing him. Meanwhile, all the other clones received the same transmission, as they killed the Jedi they were with then. Ki-Adi-Mundi and Aayla Secura were both gunned down by their clones on the planets that they were on. Meanwhile, Plo Koon was shot out of the sky by the clone troopers piloting fighters alongside him.

The clones betrayed the Jedi, who they loyally fought with for three years, as it became clear that they didn’t hesitate to kill the Jedi Generals that commanded them and fought alongside them throughout the entire Clone Wars. Of course, the consensus among fans at that time was that the clones were made to be so obedient that they didn’t have free will and would listen to Palpatine’s orders at any given time.


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But thanks to the animated ‘Star Wars: The Clone Wars’ series, we learned more about the clones. While they may have been Jango Fett clones, the clone troopers were loyal soldiers willing to die for their comrades at any moment. The most prominent out of all of the clones in that series was Captain Rex, who was a captain assigned to Anakin’s 501st Legion. Rex formed a close bond with Anakin and his Padawan, Ahsoka Tano.

Meanwhile, the other clones were also given personalities and names of their own. These clones were allowed to be unique in their own right, as it became clear that they were not just numbers that the Republic could easily dispose of.

In episode 1 of season 6 of ‘The Clone Wars,’ we saw Tup, one of the clones, suffering from a mysterious mental illness that prompted him to kill Jedi Master Tiplar out of nowhere while they were on the field. This led to an investigation that got Palpatine and Count Dooku worried about the possibility of the Jedi finding out more about this mysterious “illness.”

The clone named Fives, who was Tup’s best friend, tried to learn more about what happened to his friend, as he eventually found out that there were inhibitor chips that were grown inside the brains of the clones. These chips were biological and had been with the clones since they were embryos.

As such, they were difficult to detect as they were part of the clones’ brains. Unfortunately, Fives was killed before he could tell the truth about these chips, as the Republic and the Jedi thought he was also suffering from some sort of illness.

inhibitor chip

These inhibitor chips were, in fact, the secrets behind Order 66. That’s because the chips turned the clones into mindless soldiers that would be compelled to blindly follow Palpatine’s Order 66 once the order has been initiated. In that regard, when Order 66 was executed, the clones immediately followed it without questioning it because the chips compelled them to do so without question.

Not all clones betrayed the Jedi

While it may be true that the clones betrayed the Jedi due to the effects of the inhibitor chips in their brains, not all joined the side of the Republic/Empire in the Jedi Purge. That’s because some clones had their chips removed. Meanwhile, other clones were simply more resistant to its effects.


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The most prominent clone that didn’t kill his Jedi friends was Captain Rex, who was on the ship called the Tribunal after he accompanied Ahsoka Tano and half of the 501st Legion to Mandalore to apprehend Darth Maul. They were on their way to Coruscant when Order 66 was executed, as all of the clones of the 501st started attacking Ahsoka Tano and Maul. But before Order 66 could overcome Rex’s mind, he gave Ahsoka a clue about Fives and what happened to him.

Ahsoka researched Fives and discovered the existence of the inhibitor chip inside the clones’ brains. She could sedate Rex while all the other clones were too busy with Maul. And after allowing the Force to guide her, she removed the inhibitor chip in her loyal friend’s head, and he ended up helping Ahsoka escape the Tribunal.

headtails ahsoka clone wars

Meanwhile, during the events of ‘Star Wars: The Bad Batch,’ we saw that the Bad Batch was on the same planet as Depa Billaba and Caleb Dume (Kanan Jarrus) when Order 66 was executed. The clone started shooting Depa, who allowed Caleb to escape. However, Hunter and the other members of the Bad Batch (except for Crosshair) were confused about what was happening.

It was later revealed that the Bad Batch mutation made them more resistant to Order 66 and its effects. While Order 66 still affected them, they were still sane enough to question this order, as only Crosshair decided to attack the Jedi when he attempted to shoot the escaping Caleb Dume down. Eventually, all of the members of the Bad Batch removed their inhibitor chips to ensure that the Empire would never be able to use them to control them.

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