Star Wars: The Clone Wars – Order 66 Explained

This Star Wars article contains spoilers.

Soon, The Clone Wars will be over. The seven-season animated series is ending much in the same way as Revenge of the Sith, with the evil Emperor Palpatine rising to power and ordering the slaughter of all the Jedi. If you’ve watched the Prequel Trilogy, you know that his Jedi purge begins with Order 66.

In “Shattered,” the penultimate episode of The Clone Wars, Palpatine unleashes Order 66 on Ahsoka Tano and Maul. What was initially a major victory for Ahsoka on Mandalore has turned into a tragedy that will completely change her life.

So what is Order 66 and how is it connected to other parts of the Star Wars saga?

What is Order 66?

The order is a cue for the entire army of clone troopers to kill their Jedi commanders and any other Jedi they find. Order 66 effectively marks all Jedi as traitors to the Republic and major threats to the galaxy.

Revenge of the Sith shows several Jedi surprised by clone troopers in the middle of their missions, cut down on the ground or in the sky by their own allies. Aayla Secura, Plo Koon, and Ki-Adi-Mundi are among the Jedi who die as a result of Order 66. (Mace Windu, Kit Fisto, and others also die while dueling Palpatine on Coruscant just before the Sith Lord gives the order.)

Order 66 was hidden from everyone but Palpatine. The Jedi Temple on Coruscant is a major target of the order, as clones and Darth Vader march into the building and slaughter Jedi Knights, padawans, and younglings alike. Whether on a battlefield or at home, no Jedi is spared. 

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Ahsoka Tano gets caught right in the middle of Order 66 in “Shattered.” On her way back to Coruscant to deliver the former Sith apprentice, she suddenly feels a terrible disturbance in the Force, as Anakin joins Darth Sidious and the Jedi are slaughtered. Suddenly, the clone troopers once at her command, turn against her and try to kill her. Ahsoka is now in a fight for her life against the soldiers she once called her family.

We know Ahsoka doesn’t encounter Anakin Skywalker during Order 66. She cannot yet know that he’s become Darth Vader, as that revelation comes later in Star Wars Rebels. But she might see the end result of Order 66 for herself if she makes it back to Coruscant by the series finale of The Clone Wars.

How was Order 66 carried out?

Aren’t the clone troopers the good guys? They fought alongside the Jedi for years, after all. But the clone troopers were grown and decanted, not naturally born. They’re custom-ordered for the Republic from the gene-smiths on Kamino willing to sell people into a life of war, and Palpatine was able to make these clones a part of his long-term plan from the start. 

The “Clone Protocol 66” arc in The Clone Wars season 6 shows how an accidental early activation of Order 66 almost revealed the whole plan. When his friend killed a Jedi commander for what seems to be no reason, clone trooper Fives investigates what’s going on. His search eventually leads him right to Palpatine, where the clone guards killed him, never knowing they were serving the person who would one day be responsible for the fall of the Republic. 

As Fives discovered, every clone was implanted with a control chip that could override their free will whenever Palpatine ordered it. This was how Order 66 was possible, whether the clones wanted to follow the order or not. 

Palpatine’s plan was thorough. The creation of the clones couldn’t even be traced to him. In fact, they were thought to be the work of the Jedi. Jedi Master Sifo-Dyas had once contacted cloners about ordering the Clone Army because he saw a prophecy of what he thought was an upcoming threat the Republic needed to defend against. He didn’t live to actually place this order, but Darth Sidious and Count Dooku secretly made sure it moved ahead. That’s why the cloners expected a Jedi to come when Obi-Wan Kenobi visits them in Attack of the Clones. 

It’s a bit of a joke among Star Wars fans that Order 66 implies there are at least 65 other orders, none of which have ever been elaborated on in canon. Are they other fail-safes for Jedi uprisings? Or simply commands for clones to bring Palpatine his favorite foods? 

Who survived Order 66?

Although the massacre of the Jedi was supposed to be complete, it’s a big galaxy. Some Jedi slipped through the cracks long enough to see the rise of the Rebellion. Others lasted only a few months after the initial order. 

Both Legends continuity and the Disney canon feature Jedi who, one way or another, survived past the end of the Clone Wars. Major Jedi characters like Yoda and Obi-Wan Kenobi went into exile until the Original Trilogy, in which they tried to keep the traditions of the Jedi alive by training Luke Skywalker. Revenge of the Sith shows how both of them escaped and devised their long-term plan to one day defeat the Emperor.

Some Force users were spared if they were willing to turn to the dark side: this is where Vader and Palpatine recruited from for their league of Inquisitors, Force-sensitive hunters trained to track down the last remaining Jedi. At least one of their rank, the Grand Inquisitor, was a former Jedi Temple guard before the rise of the Empire. 

Marvel’s comic series Kanan Jarrus, follows Caleb Dume, the padawan who would one day join the group of freedom fighters at the center of Star Wars Rebels. This comic shows how Caleb survived Order 66 and later changed his name to Kanan Jarrus. In Kanan #1 by Greg Weisman and Pepe Larraz, the young Jedi and his teacher are on a mission away from the Jedi Temple, accompanied by clone troopers. Like most of the clones, they turn on the Jedi and kill Caleb’s teacher, Jedi Master Depa Billaba. By hiding at first and finding non-Jedi allies later, Caleb manages to escape the purge. He refrains from using the Force or his lightsaber in public to stay hidden in plain sight. 

Similarly to Kanan, the protagonist of the video game Jedi: Fallen Order, Cal Kestis, disconnects himself from anything that might link him to his Jedi powers or the Order. He keeps busy by working in a scrap yard but ends up back in the war almost a decade later.

Some clones also escaped. After Ahsoka had his control chip removed, Captain Rex and his fellow clone troopers Wolffe and Gregor left the Republic army and hid out on a remote world using a roving walker vehicle to stay out of sight. They eventually rejoined the war effort, this time as Rebels fighting against the Empire. 

Order 66 was perhaps the most pivotal moment in the Star Wars galaxy. The event that separated the prime of the Jedi from the decades where Force-users were scattered and in hiding has been dramatized several times before. But The Clone Wars is the closest we have to a re-telling of the events of Revenge of the Sith itself, showing how the massacre affected the characters beyond Obi-Wan, Anakin, and Yoda.