Star Wars Fanon
The time has come. Execute Order 66.
Palpatine to clone commanders

Order 66, also known as Clone Protocol 66, was one of a series of contingency orders that the clone troopers of the Grand Army of the Republic were secretly trained to prepare for during their growth. The order branded the Jedi as traitors of the Republic and called for their immediate execution without question. Its issuing by Supreme Chancellor Palpatine marked the formal beginning of the Great Jedi Purge, which started the Galactic Civil War. Almost all of the Jedi were killed by Order 66, and most of the survivors were killed in the Great Jedi Purge that followed. The Jedi Order survived through acts of Jedi, such as Obi-Wan Kenobi and Yoda teaching Luke Skywalker the ways of the Force. In 8 ABY, Order 66 was issued again and the Confederation of Free Planets began hunting the Jedi arcoss the galaxy that marked the formal beginning of the Fourth Jedi Purge.


The clone protocol

When the time comes, no one will be able to stop our plan to execute Order 66.
—Darth Sidious

Clone Protocol 66 was built into the clones of the Grand Army of the Republic during the cloning process that created them. All clones were given a bio-chip, one that could be activated by remote order via voice command; Palpatine, for example, only needed to tell clones to execute Order 66, and the order was carried out. The bio-chip, when activated, would ensure total obedience in a clone, even if that clone had strived to achieve their own individuality. The order would also cause the clones to view the Jedi as dangerous threats, ones who needed to be eliminated.

Premature execution
Jedi. Good soldiers follow orders.
—Tup, moments before executing Jedi General Tiplar

Order 66 could be found in the document entitled Contingency Orders for the Grand Army of the Republic: Order Initiation, Orders 1 through 150, GAR Document CO(CL) 56-95, a document containing a series of special contingency orders that covered any and all emergency situations, which the clones that comprised the GAR were prepared to execute, immediately and without question, and only in specific cases of extreme necessity. Some of these orders concerned contingencies any armed force could conceivably face. Many dealt with contingencies specifically involving the GAR Supreme Commander — in this case, Supreme Chancellor Palpatine — and the effect on the chain of command were he ever to become incapacitated or declared unfit to issue orders. Sufficiently buried among the other one hundred forty-nine orders so as to almost escape notice, Contingency Order 66 specifically dealt with the effect on the chain of command were issues to arise involving the Jedi.

Tiplar was killed when Protocol 66 was prematurely activated within Tup

In 20 BBY, however, the Order was nearly prematurely exposed due to a malfunction in Tup's biochip that resulted in his alternating between his regular self and entering a trance-like state, the latter of which resulted in him shooting a Jedi Master named Tiplar during a battle and forcing a Republic retreat from the planet. Darth Sidious, the alter-ego of Palpatine, as well as his Sith Apprentice Darth Tyrannus, otherwise known as Count Dooku, learned of this from Admiral Trench, and planned to have Tup abducted during a transport to Kamino to investigate his erratic behavior, realizing that his current status will most likely result in their true plans for the war, including the contingency order, being exposed to the Jedi. The ARC Trooper Fives alongside Rex and Typhuss managed to retrieve Tup, although this also resulted in the former uncovering the order and thus the conspiracy. Fives would later end up killed due to Palpatine framing him for an assassination attempt, and unable to tell either Anakin Skywalker or Rex about the contingency order, the overall conspiracy, or the Supreme Chancellor's involvement in it due to being drugged earlier.

In 19 BBY, Order 66 was issued by Darth Sidious toward the end of the Clone Wars. The official reason given for its execution was the onset of an attempted Jedi coup against the Republic; in reality, it was the culmination of a chain of events orchestrated by Palpatine himself over a period of decades, all designed to end the Jedi Order and to bring about the domination of the Sith. Just days earlier, the Senate had passed the Security Act amendment, which gave Palpatine authority to disband the Jedi Order. After the destruction of General Grievous at the hands of Obi-Wan Kenobi, Jedi Masters Mace Windu, Kit Fisto, Agen Kolar, and Saesee Tiin stormed the Supreme Chancellor's office, intent on arresting Palpatine, who had been revealed to them as the elusive Sith Lord Darth Sidious by Anakin Skywalker. Kolar, Tiin and Fisto were punctured by Sidious, but Windu was able to hold him off and eventually disarm him. Skywalker then arrived to find the Supreme Chancellor, looking defeated, attempting to surrender in exchange for his life.

When it became evident that Windu was going to kill Sidious, Skywalker intervened, which gave the Sith Lord the opportunity to destroy the Jedi Master. Windu's "assassination attempt" provided the chancellor with the excuse he needed to have Order 66 carried out. Anakin Skywalker, for his part, was in a state of shock and confusion. Sidious, now scarred from the "attempt on his life," took advantage of young Skywalker's emotional distress and pressured him to turn to the Dark side of the Force. Unsure what to do, feeling he could never be forgiven for what he had done and desperate to save his wife Padmé Amidala from the possibility of a presaged demise, Skywalker complied and was "knighted" by Sidious as his new apprentice, Darth Vader, Lord of the Sith. Vader would have an important role to play in carrying out his new master's plan.

Execution of the Order
Every single Jedi, including your friend, Obi-Wan Kenobi, is now an enemy of the Republic.
—Darth Sidious to Darth Vader

Obi-Wan Kenobi and Boga fall into an Utapaun sinkhole after the execution of Order 66

At 2100 hours local time, on the one thousand, eighty-ninth day of the Clone Wars, Palpatine retired to his private office in the Republic Executive Building, activated his comm unit and, with much relish, issued the command for which the Sith had spent a thousand years waiting: “Execute Order 66”, thinking to himself that his only regret was that he couldn't be there personally to watch them die. He employed a channel that would make the authenticity of the order unquestionable, but ironically, the signal was encrypted using a Separatist code – one of the rare giveaways that he was in fact the hidden hand behind both sides of the war. Palpatine sent word out via the office of the Chancellor to all of the clone commanders in the army. The commanders displayed a variety of reactions to the surprising order, but since it came from the Chancellor himself, virtually all of them carried it out without question or hesitation. On countless planets, Jedi were cut down by their troopers. The Jedi, who had been spread throughout the galaxy across disparate battlefields, were almost all caught totally unaware and easily gunned down. Three years of non-stop galactic warfare polluted the Force with the dark side, clouding Jedi perception even further. Because the clones had no malice nor hatred, but were merely following a legal order, they had no ill intent in their heart, which might have given some warning to the Jedi via the Force.

Although it was impossible for Palpatine to have issued the order to every single commander individually, he did take the time to contact several personally before the Order was relayed throughout the army as a whole. Within the first minutes of the Order, several members of the Jedi Council had been killed; including Plo Koon on Cato Neimoidia at the hands of Captain Jag, Stass Allie on Saleucami at the hands of Commander Neyo and CT-3423, Aayla Secura on Felucia at the hands of Commander Bly, Commander Typhuss and members of the 327th Star Corps, 52nd Star Corps, Alpha Company, 42nd Assault Squad and Ki-Adi-Mundi on Mygeeto by Commander Bacara and the Galactic Marines. On Utapau, Obi-Wan Kenobi was riding a varactyl named Boga when Commander Cody executed the order, ordering an AT-TE to fire on him, but Kenobi managed to survive and escape the planet. He soon reunited with Grand Master Yoda, who had also managed to escape an attack by Commander Gree on Kashyyyk.

As noted, not all clone troopers obeyed the Order. On Murkhana, Roan Shryne and Olee Starstone were rescued from Order 66 by members of a clone commando unit. Led by Climber, they initially questioned the validity of the order, and even upon confirmation, refused to side with the government over those who had fought alongside them, having developed an affinity for the Jedi. Omega Squad, Delta Squad, and Ordo Skirata did not even hesitate to disobey the order, though all of them feign compliance to avoid suspicion, as they had already formed doubts about Palpatine and his new Centax Clones. Captain Maze, as well, did not execute Arligan Zey. In all other recorded instances, Commandos and ARC troopers obeyed it.

Raid on the Jedi Temple

Raid on the Jedi Temple

On Coruscant, Senate Emergency Response announced a state of martial law over Coruscant, and declared the Jedi Temple under military lockdown. Order 66 authorized the newly christened Darth Vader and the 501st Legion to attack the Jedi Temple; however, deciding to take a more surprise-attack approach, a mission named Operation: Knightfall was devised where the 501st attacked any Jedi they found in the Temple — Masters, Padawans, even younglings. They also massacred non-Jedi staff, including administrators, trainers, and guards. Bail Organa was able to escape because the 501st were "tired of killing". No Jedi within the building were spared, but some escaped, including Shaak Ti, Kazdan Paratus and Jin-Lo Rayce.

Missing in action

There were many Jedi whose fate after Order 66 remained unknown. In the chaotic circumstances in the early days of the Empire, there were many reasons why the fate of certain members of the Order remained unclear, chiefly among these reasons being that that either no body could be discovered or the troopers tasked with the execution had been killed. Among the missing were Depa Billaba, who was believed to be recovering from past wounds at the time of the attack on the Jedi Temple and Master Coleman Kcaj, a member of the Jedi Council, was also believed to have been present on Coruscant during Operation: Knightfall. It was assumed by Obi-Wan Kenobi that his long time friend, Bant Eerin, was killed. Other Jedi whose fates were lost in the confusion were Glynn-Beti, Ulu Ulix, Voolvif Monn, Pix and Saldith.


The remaining Jedi will be hunted down and defeated!
—Palpatine, before the Galactic Senate

Although Order 66 greatly depleted the Jedi Order's ranks, with an estimated less than 100 Jedi surviving it, it was only the beginning of the Great Jedi Purge, which stretched on for years. Nearly all of the surviving Jedi Knights were hunted down and murdered by Darth Vader, while Order 66 itself remained in effect indefinitely among the ranks of the Galactic Empire's newly-christened stormtroopers. Masters Kenobi and Yoda, like many others, chose to go into exile—on Tatooine and Dagobah, respectively. There they managed to elude Imperial forces for many years; a feat few of their contemporaries could claim.


A young Jedi named Darth Vader, who was a pupil of mine until he turned to evil, helped the Empire hunt down and destroy the Jedi Knights… Now the Jedi are all but extinct.
—Obi-Wan Kenobi tells Luke Skywalker about the fall of the Jedi

For nearly twenty years, the Empire was able to expand without any significant Jedi opposition. Shortly before the Battle of Yavin, however, Kenobi emerged from his exile and began training Luke Skywalker to become a Jedi Knight, in the hopes that Luke would be able to defeat Vader and the Emperor. Kenobi was killed by Darth Vader aboard the Death Star, leaving Luke to be trained by Yoda, the only known surviving Jedi. The two trained on Dagobah before Luke left to confront Vader, and Luke did not return until just before Yoda's death.

The redemption of Anakin Skywalker led to the return of the Jedi

Upon the Jedi Master's death, Luke became the last of the Jedi and set out to confront Vader once more, now having learned the truth that Vader was his father. During the Battle of Endor, Luke redeemed his father, and Anakin killed the Emperor. The act of killing the Emperor resulted in Anakin's death, leading to the end of the Sith; through his death, Anakin fulfilled the prophecy of the Chosen One and brought balance to the Force. By confronting his father and saving him, Luke became the first new Jedi Knight in a generation, bringing about the return of the Jedi.

Second Order 66

The second Order 66

In 8 ABY, Order 66 was issued again and the Confederation of Free Planets began hunting the Jedi arcoss the galaxy that marked the formal beginning of the Fourth Jedi Purge. The purge officially began with Order 66, which declared the Jedi enemies of the Confederation and ordered the Confederate Army to turn on them. Another reason cited for wiping out the order was the argument that they were complicit in starting the Second Yuuzhan Vong Invasion to destabilize the galaxy and overthrow the government. Facts stated in support of this argument included the Jedi involvement in initiating a rebellion against the Confederation.

Simultaneously, the Confederation dispatched the Coruscant Guard, the 52nd Star Corps, Delta Squadron, Alpha Company and the 42nd Assault Squad, the 212th Attack Battalion and the 501st Legion to eradicate all the Jedi in their Temple on Coruscant. The Confederation justified its purge with a conspiracy of the Jedi Order's attempt to take control of the Confederation by assassinating the head of government.

Shortly after the attack on the Jedi Temple and Order 66, the CFP was turned into the New Galactic Empire, who continued the CFP's efforts to hunt down the Jedi and their supporters.

Afterwards, the Jedi who survived the attack on the Temple and Order 66 went on and formed the Jedi Holdouts. After several initial victories, they lost, and most of the Jedi who survived went into hiding, while others were killed. The Remnant to Restore the Republic was formed, but was also destroyed.

The Second Jedi Rebellion started when a group of surviving Jedi attacked the Empire. There were several battles in the war. The Emperor was a traitor and was on the Jedi side. In 12 ABY the Empire attacked the New Jedi Temple while it was under construction by the Jedi Remnant and the Remnant to Restore the Republic. The attack was led by CC-2009, Draco Malfoy, CC-1010, and CM-9797. It was an Imperial victory and the temple was destroyed. During the battle, it was discovered that the Galactic Emperor was a traitor and was dealing with the Jedi. He was found and killed during the battle.

Known clone commanders

Jedi victims

Clone victims

Clones killed by Jedi or Clones during Order 66

Known survivors

Known units that were in Order 66

External links