In Revenge of the Sith, the Clones turned on the Jedi and wiped almost all of them out. This moment was a major turning point in the Star Wars movies.
When Palpatine said, “Execute Order 66,” he initiated his secret plan to have the Clones betray the Jedi and allow him to emerge as Emperor.
Why did the Clones follow it so easily? The main reason is that it was beyond their control.
Who Were the Clones?
Toward the end of the Galactic Republic, an army of Clone troopers was developed on the planet Kamino to protect the Republic. This army was forged through the cloning of Jango Fett’s genetic template.
At the Jedi’s request, the Kaminoans, who specialized in cloning, built this clone army. However, the cloning initiative secretly turned to Sith purposes.
The Republic troopers were trained soldiers that were designed to fight better than battle droids. The Clone Wars took its name from these clone troopers who battled the Separatist Droid Army, led by General Grievous. In turn, Grievous took orders from Count Dooku who sought to break away from the Republic.
The clone troopers fought the droid army for three years and were about to defeat them when Emperor Palpatine emerged and issued Order 66.
What Was Order 66?
During the Clone Wars, the Republic was at war with the Separatists, and the Senate granted Chancellor Palpatine emergency powers. Palpatine also worked behind the scenes to lure Anakin Skywalker to the dark side to launch his Empire.
Once Obi-Wan Kenobi defeated General Grievous, Palpatine was supposed to surrender his powers. But Palpatine emerged as a Sith Lord and killed Jedi Master Mace Windu after Anakin intervened. Once the plan to arrest or kill Palpatine failed, Anakin transitioned to Darth Vader and Palpatine issued Order 66.
Also called Clone Protocol 66, Order 66 was a secret order that specified that the Jedi were traitors to the Republic and needed the Clone Army, or Grand Army of the Republic, to execute them.
All clone troopers had this order programmed into their behavioral modification biochips set inside their brains. The Kaminoans were not aware of this purpose, nor were the Jedi.
Why Did the Clones Betray the Jedi?
As Clones, they were programmed to obey orders, and this is part of the reason why they betrayed the Jedi. Palpatine also installed chips in them to ensure they followed commands without question.
The Kaminoans, who created the Clones during the third stage of their development, implanted these inhibitor chips, or behavioral modification biochips. The inhibitor chips compelled the Clone Troopers to follow orders and were also used on enslaved Wookiees.
Once Palpatine issued Order 66, the Clones had no choice but to obey him. Even those Clones who did not agree with the order had to follow it.
The inhibitor chips drive the explanation here. Not only do the chips make the Clones follow orders, but they erase existing beliefs like friendships and alliances with the Jedi.
As artificially created beings, the Republic controlled the Clones, but Palpatine controlled them more directly. They had been forged to follow orders and that was what they did. The inhibitor chips served as the main conduit, though, for Palpatine to compel the Clones to follow Order 66.
Perhaps the Jedi could have removed the inhibitor chips and saved themselves. Not likely because, as fans have stated, the Jedi were told that the chips were installed to prevent the Clones from being too aggressive.
Palpatine fooled the Jedi and the Republic about the Clones’ intentions. Palpatine pulled off his master plan, and they were forced to go along with it.
Why did the Clones Follow Order 66 So Easily?
In Revenge of the Sith, we see the Clones turn against their one-time allies, the Jedi, without hesitation. Clone troopers rapidly go from battling with the Jedi to massacring them. It’s so rapid that we might conclude that their actions were voluntary.
As the Legends series Republic Commando depicts, the clone troopers could have been taught this order and not merely forced to obey it. From this non-canon perspective, the tensions between the Jedi and Clones may have helped lead to this catastrophic moment.
Yet, this betrayal was more likely not as easy as depicted. One of the tragedies of Order 66 is that the clone troopers could not “stop themselves from turning on their leaders and friends.”
We do not see the Clones’ inner conflict in the movie, but we did see how closely they worked with the Jedi. This relationship is more apparent in The Clone Wars series too. Hence, the Clones were unwilling participants in this betrayal.
That they would have preferred to resist the order if they could is demonstrated by how some Clones refused to follow it.
Did Any Clones Refuse to Obey Order 66?
Despite their training and chip programming, some clone troopers disobeyed Order 66. The Clones Wars animated show had a trooper named Cut Lawquane who escaped from the Battle of Geonosis and did not follow the order. He eventually met another Clone that refused to obey Order 66.
Captain Rex is perhaps the best-known Clone who did not follow Palpatine’s orders. Rex was second-in-command to Anakin Skywalker and later a Commander of the Rebel Alliance. His story of defiance came out in The Clones Wars and The Bad Batch.
Fives is another clone trooper who figured prominently in The Clone Wars series. He removed his own inhibitor chip, while Ahsoka Tano removed Rex’s. Without their inhibitor chips, Fives and Rex refused Order 66.
Fives, or CT-5555, investigated the inhibitor chips and the death of a Jedi at the hands of the Clone Tup. Fives was killed before he could reveal the truth about Order 66.
Kix and Maze were other Clones that disobeyed the Order once their chips were removed. Many more would have done the same if given the chance.
As The Bad Batch show depicts, some Clones had genetic mutations that came with immunity to the inhibitor chips, allowing them to disobey the order.
If there had been more Clones like Clone Force 99, Order 66 would not have transpired the way it did.
The Clones Betrayed the Jedi
The Clones betrayed the Jedi so easily because of how they were created and because of the inhibitor chips installed in them. They could not resist the order implanted into their brains.
Only those who had those chips removed defied Order 66. By doing so, those Clones became legendary in the Star Wars universe.
Todd Wahlstrom is a creative and analytical freelance writer and life-long Star Wars fan who has expanded into writing about the Marvel Cinematic Universe. He has written about recent shows such as The Mandalorian and Andor and classic topics like Darth Vader, the Jedi, and Boba Fett. His recent articles include the MCU’s Iron Man, Captain America, and Thor. Todd is the author of a non-fiction book, holds a Ph.D. in history, and enjoys hiking, running, and reading about science.