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Star Wars: The history of Order 66 explained

Order 66 is an infamous part of Star Wars' mythology. This command is the top secret order that Chancellor Palpatine gives to all clone troopers in Revenge of the Sith, which dictates that all Jedi are traitors to the Galactic Republic and subject to summary execution. In the wake of the mass slaughter of Jedi that follows, Palpatine transforms the Republic into the Galactic Empire. He goes on to rule the galaxy until his apprentice, Darth Vader, kills him at the end of Return of the Jedi.

While Order 66 is a major event in the Star Wars universe,  even the most diehard fans might not know everything that happened before, after, and even during this calamitous event. And as Star Wars media such as books, comics, and even television continues to expand upon what instigated the Great Jedi Purge, there's always more to learn. We're here to break down the how and why of Order 66, from the technological groundwork that enables it to the clone troopers who disobey it.

Inhibitor chips

As the last two seasons of Star Wars: The Clone Wars reveal, many clones are quick to follow Order 66 because of inhibitor chips in their brains. These chips erase any existing biases or beliefs, including ones about Jedi comrades, and enforce total obedience.

Jedi Master Sifo-Dyas, who commissioned the clone army for the Republic, gave the Kaminoans, who create the clones, the original control chip. The chips initially make the clones less aggressive than their template, Jango Fett, and act as a safeguard against renegade Jedi. After Darth Sidious and Darth Tyranus (or Count Dooku as he is more commonly known) have Sifo-Dyas killed, however, they take over the project and keep the inhibitor chips a secret from the Jedi Council. The two Sith Lords also lead the Kaminoans to continue believing that the chips are a contingency plan against renegade Jedi.

These behavioral chips are extremely hard to find, as they are microscopic in size. In the Clone Wars episode "Conspiracy," for example, a clone named Tup's chip is only found after the medical droid AZI-3 performs a level five atomic brain scan on him. Additionally, the second-to-last episode of The Clone Wars shows that former Jedi Ahsoka Tano cannot find Clone Commander Rex's biochip with the standard medical facilities onboard a Venator-class Star Destroyer, until she uses the Force to locate it. Who knew that a device this small could cause a major galactic catastrophe?

A premature execution

Although Sidious is mostly successful at keeping his plans hidden from the Jedi, they are almost unearthed in season six of The Clone Wars.

In the episode "The Unknown," during a battle to retake the planet Ringo Vinda from Separatist occupation, a clone trooper named Tup succumbs to some sort of trance and kills a Jedi General named Tiplar. Anakin Skywalker, who also leads the clones in that battle, believes that Tup's irrational behavior is part of a Separatist plot and sends him back to Kamino for a more thorough inspection. 

The following episode, "Conspiracy," sees Tup's best friend Fives, an Advanced Recon Command trooper who accompanied Tup on his transport, team up with medical droid AZI-3 to break protocol and diagnose Tup's condition. They eventually discover a "tumor" in Tup's brain, which AZI-3 extracts. Shaak Ti, a Jedi Master who is stationed on Kamino during this episode, proposes to Chancellor Palpatine that this tumor receive further inspection at the Jedi Temple, while Palpatine suggests that it be sent to state-of-the-art Grand Republic Medical Facility. Nala Se, the Chief Medical Scientist on Kamino, backs up the chancellor's idea, so Ti has no choice but to accept it.

Investigating the "tumor"

Fives remains suspicious about the cause of Tup's death, and investigates it in two particular episodes of The Clone Wars. At the beginning of the episode "Fugitive," Fives espouses the belief that he is returning to the front line. But AZI-3 tells him in passing that actually, his mind will be erased, and he will be placed on sanitation duty in Kamino. This prompts Fives to escape custody and investigate the tumor with AZI-3. After the medical droid successfully removes Fives' perfectly intact chip, they go to the embryo room and discover that these inhibitor chips are implanted into all clone embryos at stage three of their development. Fives reveals his findings to Shaak Ti and she decides to send him and the extracted chips to be presented to Chancellor Palpatine. 

The following episode, "Orders," sees Fives framed for attempting to assassinate Palpatine and forced to go on the run in Coruscant. With the help of Fives' fellow clone Kix, both Anakin and Rex meet Fives at an underground warehouse where he traps them in a ray shield and tells them that these chips are part of larger conspiracy to wipe out the Jedi. Unfortunately, Clone Commander Fox barges in and kills Fives after he tries to reach for one of Rex's discarded pistols. It's a devastating loss, a tremendously powerful episode, and a key step on the bloody road to Order 66.

Kix continues the search

The canonical short story "The Crimson Corsair and the Lost Treasure of Count Dooku" reveals what happens to Kix after the events of "Orders." Kix does some digging and finds out the truth about the clones' inhibitor chips. Before he can tell anyone, however, Count Dooku has Kix kidnapped and interrogated. Since he won't tell his interrogators anything, Kix is frozen in a cryo-cycle stasis pod and put on the Obrexta III cruiser, to be brought to Dooku himself. When a Republic ship attacks the Obrexta III, the B1 battle droid piloting the ship is so dedicated to making sure no one finds this prisoner that it jumps through hyperspace to a random sector, where the Republic cannot find them. 

Fifty years later, Sidon Ithano and his pirate crew find the crashed Obrexta III on the desert planet Ponemah. They unfreeze Kix, who tells them everything and subsequently joins their crew. Kix failed in his attempt to tell the Jedi Council about Order 66 in time, but at least he finishes what Fives started.

Removing the chip

Some clones do manage to remove their inhibitor chips, and do not have to participate in Order 66 as a result. After the events of "Orders," Rex files a confidential grievance report about how the inhibitor chips inside the clones' heads have an unknown purpose. He knows this report will likely be ignored, but presses forward with it regardless. In the wake of Order 66, however, Rex resists the chip's effects long enough to tell Ahsoka to "find Fives," before he succumbs to its influence and shoots at her. With the help of three astromech droids, Ahsoka finds Rex's report and uses it to remove the inhibitor chip inside his brain. The two then fight their way out of the Venator-class Star Destroyer and escape before it crashes on an unknown moon. Ahsoka and Rex part ways after burying every victim of the crash they can find. 

Rex eventually joins up with two other Clone Commanders who have also removed their chips. These three retired clones eventually meet with the Ghost crew in Star Wars Rebels, and Rex ends up aiding the Rebel Alliance in their fight against the Empire. As a rebel, Rex reunites with Ahsoka and continues to prove his worth, even in his old age.

Clone Commander Grey disobeys orders

Shockingly, a Clone Commander named Grey questions Order 66 without having to remove his inhibitor chip. In the 2015 comic Kanan: The Last Padawan #5, Grey and Clone Captain Styles are about to kill their former Jedi friend Caleb Dume, who later changes his name to Kanan Jarrus. He pleads with them that Palpatine is the real traitor, not the Jedi. With the clones distracted, Caleb uses the Force to escape into space and enter the nearby Kasmiri, one of two starships, the other being Escape, that arrives to save him.

While Styles is determined to destroy the enemy freighters, Grey begins to regret killing Caleb's master, Depa Billaba, and describes following Order 66 as if he was under a spell that robbed him of free will. As the weakened Kasmiri and Escape charge at the clone freighter, Grey opens fire on the bridge crew, which deactivates his freighter's shields and allows the other two ships to destroy it. Tragically, Kanan never learns of Grey's sacrifice and becomes distrustful of clones as a result. In the end, Grey's consciousness supersedes his secret conditioning and he dies protecting a Jedi he was ordered to kill.

Life after Order 66

So, what happens to the clone army after Order 66? As the Republic quickly transitions into the First Galactic Empire, all remaining clone troopers are re-designed into Imperial stormtroopers. After the last batch of clones is commissioned, the Empire discontinues cloning operations on Kamino and slowly phases clones out of military service. There are a variety of jobs the clones are filtered into from here on out. The second issue of the comic series Darth Vader: Dark Lord of the Sith shows clones on a Jedi outpost called Brighthome taking inventory of every Jedi weapon and artifact onboard. Some particularly lucky clone troopers serve as Imperial Royal Guards, one of the best jobs available. 

Although some clones remain in military service as late as the Battle of Yavin, many of them are retired and replaced with human conscripts and recruits. When asked at a San Diego Comic-Con panel in 2014 about why clone troopers are phased out for stormtroopers, Clone Wars and Rebels producer Dave Filoni explained that the clones' accelerated aging generally makes them unfit for fighting, as their skills and life force deplete rapidly. This is tragic, to say the least. They deserve so much more, especially after everything they go through over the years.

Those who foresee Order 66

Believe it or not, some Jedi foresee the Great Jedi Purge. In the audiobook Dooku: Lost Jedi, Sifo-Dyas' master, Lene Kostana, takes him and Dooku to the forest planet Asusto, so that they can retrieve a Sith artifact. After Dooku cuts down nearby smugglers in a fit of rage, the three Jedi are engulfed in moss and end up in a dark cavern where their feet are restrained. Their captors are the Presagers of Hakotei, a ritualistic cult that has sacrificed millions in exchange for visions of the future. Suddenly, the moss begins to consume the Jedi, which causes Dooku to see several visions of the future. One of these visions shows clones killing a Jedi named Jor Aerith. Dooku is so entranced by these visions that he unknowingly uses Force lightning to kill the Presagers, as well as free himself and the other Jedi.

As Lene tries to comfort Dooku about what he saw, the two Jedi spot Sifo-Dyas suffering through seizures as he continues to experience visions. Once he is out of his trance, Sifo-Dyas explains, "Master, there were soldiers ... hundreds of thousands of soldiers. So much blood ... washing over me, washing over us all." This description, while vague, likely refers to Order 66. Either way, Lene makes sure that neither Sifo-Dyas nor Dooku tells the Jedi Council about what they saw on Asusto.

Darth Vader and the Inquisitors

Even after Order 66 is executed, many Jedi still live throughout the galaxy. But Palpatine has a plan for them.

In the 2017 comic Darth Vader: Dark Lord of the Sith #6, Palpatine puts Vader in charge of the Order of Inquisitors, a group of Force-sensitive agents tasked with hunting down any Jedi who survived Order 66. Although several Inquisitors first appear in Star Wars Rebels, the Dark Lord of the Sith comic series takes a much more detailed look at the origins of their respective relationships with Vader. Since the Inquisitors are all former Jedi, Vader notices that they still fight defensively. He decides to change this the hard way. As part of his first training sessions, several Inquisitors have at least one part of their body severed so that Vader can teach them a lesson about loss.

Each Inquisitor has their own unique set of skills. For example, the Ninth Sister is strong in reading emotions, and the Tenth Brother has exceptional hearing and intuition, even though he lacks eyes. Unfortunately, many Inquisitors are not skilled enough to take on powerful Force-users such as Ahsoka and Maul. Nevertheless, some Inquisitors are still successful in their hunting. The now defunct canon mobile game Star Wars: Uprising reveals that an unnamed Inquisitor manages to kill four Jedi in the Anoat sector.

A Jedi initiates Order 66

Issues 13 through 17 of Darth Vader: Dark Lord of the Sith see Vader and three Inquisitors (Sixth Brother, Ninth Sister, and Tenth Brother) travel to the planet Mon Cala in order to hunt down a refugee Jedi named Ferren Barr, who is supposedly advising Mon Cala's king Lee-Char. While Vader and the Inquisitors are in pursuit of Barr, Tarkin requests Vader capture King Lee-Char, and therefore end the ongoing conflict on Mon Cala. Vader accepts and leaves Barr to the Inquisitors, who corner Barr and his last remaining disciple into a dead end.

At this moment, Barr unmasks the purge troopers who have accompanied the Inquisitors. He notices that they are all clones commissioned after the Jedi Purge and uses the force to activate Order 66. This causes the troopers to open fire on their Inquisitors, as the Inquisitors are all former Jedi, and allows Barr and his acolyte to escape. The Tenth Brother is killed, but the Sixth Brother and Ninth Sister Force-push the troopers to the slide. As they flee, however, the Sixth Brother severs the Ninth Sister's left leg and leaves her to fend for herself. Perhaps this scene is another reason the Empire ultimately retires the clones.