Order 66 Order 66 was an event at the end of the Clone Wars in which the clone trooper s of the Grand Army of the Republic turned against their Jedi commanders and terminated them , bringing about the destruction of the Jedi Order . The event was triggered by Clone Protocol 66 , an order implanted into the clones by the Sith Lord s and Kaminoan scientist s who created the clone army ( the latter being tricked by the Sith into thinking that the sole purpose of their hidden " programming " was to install a safeguard against rogue Jedi ) . The protocol caused clone trooper s to violently lash out at the Jedi and to view them as traitors , and were controlled by a bio - chip implanted into the clones during their creation ; the chip could control the behavior of the clones and ensure total obedience . The conspiracy , led by Supreme Chancellor Sheev Palpatine — secretly Darth Sidious — and Count Dooku , was nearly exposed when the chip belonging to clone trooper CT - 5385 malfunctioned , but all who learned of the conspiracy were killed . In the final days of the Clone Wars , after having revealed himself to the Jedi as the Dark Lord of the Sith , Palpatine issued Order 66 . The clone troopers throughout the galaxy turned on the Jedi and began killing them , with numerous Jedi perishing on battlefields across many different worlds . Meanwhile , the fallen Jedi Knight Anakin Skywalker , who had become the Sith Lord Darth Vader , marched on the Jedi Temple with the 501st Legion and killed the Jedi within it . Although most Jedi were wiped out , a small number of Jedi — including Obi - Wan Kenobi , Yoda and Kanan Jarrus — were able to escape , Order 66 marked the destruction of the Jedi , forcing the survivors into exile for over two decades until the defeat of the Sith . Description . Clone Protocol 66 was built into the clone trooper s 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 ; Sheev 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 , erasing existing biases and beliefs . The order would also cause the clones to view the Jedi as a dangerous threat that needed to be eliminated at all costs . History . Prelude . Around ten years prior to the outbreak of the Clone Wars , Jedi Master Sifo - Dyas ordered the clone army for the Galactic Republic . As part of the Sith plot to destroy the Jedi Order , Count Dooku — a Sith Lord who posed as a Jedi to the Kaminoan cloners — provided the Kaminoans with a bio - chip to be implanted into the clones during the early phase of their growth period . This chip contained clone protocol 66 which , when activated , would ensure total obedience in the clones and cause them to violently lash out against the Jedi . Towards the end of the war , Order 66 was almost prematurely exposed due to a malfunction in the bio - chip inside of clone trooper CT - 5385 , nicknamed " Tup , " resulting in his alternating between his regular self and entering a trance - like state . The latter state caused Tup to shoot Jedi Master Tiplar during the battle of Ringo Vinda , killing her instantly . The Republic retreated from their offensive , and prepared to study Tup to determine what happened . Dooku and his master , Darth Sidious — secretly Supreme Chancellor Palpatine — learned of what happened to Tup and feared that he would lead the Jedi to discovering their true plan for the war , including the clone protocol . The Confederacy of Independent Systems tried to kidnap Tup from the Republic , but the Republic succeeded in bringing him to Kamino for further study . The Kaminoans , knowing the truth about the clone protocol , studied Tup and claimed that it was a virus that caused him to kill Jedi General Tiplar . Fellow trooper CT - 5555 , nicknamed " Fives , " did not believe their claims and discovered the chip inside of Tup . With the help of the medical droid AZI - 3 , Fives also discovered the chip inside of his head , and AZI - 3 removed it for study before they both discovered that the chip was inside all of the clones . The Jedi brought Fives to Coruscant for further examination , where Fives came face - to - face with Palpatine and discovered that the Chancellor was behind the plot . Palpatine framed Fives for an assassination attempt , discrediting the clone and causing the Jedi and fellow clones to pursue Fives . Despite knowing the truth , Fives was unable to tell Anakin Skywalker or Clone Captain CT - 7567 , who were with him in the end , about the conspiracy or the Supreme Chancellor ' s involvement before being killed . The Jedi Order accepted the story that it was a virus that caused Tup and Fives ' behavior . Later , the Jedi discovered that the Sith were behind the creation of the Grand Army of the Republic , as Count Dooku — under the name Tyranus — had personally selected Jango Fett as the genetic template for the clones and had worked with the Kaminoans to create the army after it was ordered by Sifo - Dyas . At the insistence of Grand Master Yoda , who testified to the clones ' loyalty and valiant service , the Jedi High Council chose to not disclose the conspiracy to the public or even the Supreme Chancellor , believing that the Republic would lose the public ' s trust if it became known that Dooku was involved in the creation of the clone army . Shortly thereafter , Yoda went on a journey to discover the secrets of immortality , and , on Dagobah , saw a vision of what would become Order 66 . Throughout his journey , Yoda came to accept that the Jedi would likely lose the Clone Wars , though he did not know how . He did , however , believe that the Jedi would still ultimately triumph in the long - run . Execution . With the secrets of Order 66 secure , Palpatine and Dooku continued with their plans during the Clone Wars . By the war ' s end , public support for the Jedi had weakened due to their management of the conflict , while Palpatine remained a popular figure . After the deaths of Count Dooku and General Grievous , which the Jedi hoped would end the war , Palpatine revealed himself to Skywalker as the Dark Lord of the Sith in an effort to seduce him to the dark side of the Force . When Skywalker informed Jedi Master Mace Windu of the Chancellor ' s identity , Windu assembled a team composed of himself , Kit Fisto , Agen Kolar , and Saesee Tiin , to arrest Palpatine . Their attempt led to a lightsaber duel in which Palpatine killed all four of the Jedi , and Skywalker turned to the dark side . Palpatine used the duel as a pretext for declaring that the Jedi were traitors , ones who had attempted to assassinate him and take control of the Republic for themselves . The Chancellor issued Order 66 to various Clone Commander s across the galaxy , while Skywalker — now the Sith Lord Darth Vader — was sent to kill the Jedi within the Jedi Temple . Thousands of Jedi throughout the galaxy were killed including Ki - Adi - Mundi , Aayla Secura , Plo Koon , Stass Allie , and even youngling s . Aftermath . The execution of Order 66 marked the destruction of the Jedi Order . Before the Galactic Senate , Palpatine told the galaxy that the Jedi were traitors who had attempted to kill him and seize power , and the destruction of the Jedi was greeted with applause by the Senate . Having amassed immense central authority during the war , and without the Jedi Order standing in his way , Palpatine transformed the Republic into the Galactic Empire and declared himself Emperor . Along with Vader , Palpatine ' s rule meant that the Sith plan was completed , and the Sith Lords once again ruled the galaxy . Some clones , however , were able to remove the control chips in their head such as Captain Rex , Commander Wolfe , and Captain Gregor , which allowed them to disobey Order 66 . Few Jedi survived the onslaught of Order 66 . At least one member of the Jedi Temple Guard survived by submitting to the Sith , becoming Grand Inquisitor of the Inquisitorius . Jedi Master Luminara Unduli was captured and later executed at the Spire on Stygeon Prime . Obi - Wan Kenobi went into exile on Tatooine , along with Vader ' s infant son , Luke Skywalker ; Vader did not know that Luke or his twin sister , Leia , had been born , so the twins were taken into hiding . Grand Master Yoda , meanwhile , went into exile on Dagobah . Padawan Caleb Dume took on the name " Kanan Jarrus " and went into hiding , giving up his identity as a Jedi for fourteen years before returning , with the crew of the " Ghost " , to rebel against the Empire . Despite having left the Jedi order , Skywalker ' s former Padawan Ahsoka Tano was also targeted by Order 66 . However , she along with Captain Rex were able to fend off clone troopers and escape , faking their deaths in the process and going into hiding in the Outer Rim . Jedi Archives librarian Jocasta Nu also managed to survive . Legacy . For nearly twenty years , the Empire was able to expand without any significant Jedi opposition . Approximately five years before the Battle of Yavin , however , surviving Jedi , the very few remaining in the galaxy , begun to actively aid rebel cells around the galaxy , such as Kanan Jarrus for the Spectres and Ahsoka Tano for a larger network of rebel cells . Years later , 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 Emperor Palpatine . Kenobi was killed by Darth Vader aboard the Death Star , leaving Luke to be trained by Yoda , one of 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 . 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 Darth Sidious . The act of killing Emperor Palpatine 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 . Thirty years later , Luke ' s nephew Ben Solo , now known as Kylo Ren , carried out a similar incident , causing Luke to go into exile on the planet Ahch - To . Behind the scenes . The events of Order 66 , namely the destruction of the Jedi Order , were first mentioned in . The destruction itself was first depicted on - screen in , while the backstory of Order 66 was provided in a four - episode arc in the television series " " . The of the ongoing comic series " " , featuring Kanan Jarrus of the series " Star Wars Rebels " , depicts Order 66 and its aftermath . This aftermath is further explored in " Star Wars Rebels " , as Kanan deals with passing on the legacy of the Jedi in the wake of the Order ' s destruction .