Order 66, also referred to as Clone Protocol 66, Protocol 66, or simply "the Order," represented one of the most confidential contingency orders. This directive designated all Jedi as traitors to the Galactic Republic, thereby authorizing their summary execution by the Grand Army of the Republic. Integrated into the Army's clone troopers via behavioral modification biochips implanted in their brains, the order rendered it nearly impossible for the clones to defy the command to turn against their Jedi Generals. The Kaminoan scientists responsible for designing the clone troopers believed its application would be limited to scenarios involving rogue Jedi. However, Order 66 served as the covert mechanism by which the Sith aimed to orchestrate the long-awaited downfall of the Jedi Order.
The Sith's clandestine agenda during the Clone Wars progressed largely undetected until a premature activation of Order 66 led to the death of General Tiplar. This occurred when Tup, a clone with a defective biochip, malfunctioned and betrayed his Jedi officer. This event prompted ARC trooper Fives to launch his own investigation, suspecting a Separatist plot against the Republic. However, on the galactic capital of Coruscant, he discovered that the chips were designed to condition the clones to become hostile towards the Jedi. Moreover, he uncovered the involvement of Supreme Chancellor Sheev Palpatine in the conspiracy to some degree and attempted to assassinate him. Fives shared his findings with his Jedi superior, Anakin Skywalker, but before he could provide definitive proof, he was killed by clone shock troopers of the Coruscant Guard.
Despite the Jedi High Council's growing suspicion of the Chancellor's intentions, the plan proceeded unabated for the remainder of the war. In 19 BBY, a contingent of Jedi Masters attempted to arrest Palpatine after uncovering his true identity as the Sith Lord Darth Sidious. Following the failure of their attempt, Palpatine exploited the situation to accuse the Jedi Order of treason. He then forcibly compelled the clone army to execute their Jedi commanding officers in accordance with Order 66.
Across the galaxy, countless Jedi were betrayed and murdered by their own troops. Simultaneously, the Chancellor's new apprentice, the Sith Lord Darth Vader, formerly Jedi Knight Anakin Skywalker, spearheaded the 501st Legion in a direct assault on the Jedi Temple on Coruscant. With the exception of a handful of Jedi survivors, including Grand Master Yoda, Jedi Master Obi-Wan Kenobi, former Padawan Ahsoka Tano, Padawans Kanan Jarrus and Cal Kestis, and Jedi Knight Cere Junda, the Great Jedi Purge was largely accomplished through the initial activation of Order 66. Even after the initial onslaught, Order 66 remained in effect, mandating the immediate execution of all Jedi, or even those suspected of being Jedi. Sidious subsequently solidified his reign as Emperor of the Galactic Empire, ruling for decades until the prophecy of the Chosen One was fulfilled, marking the end of the Sith and the restoration of balance in the Force by 4 ABY.

The clone troopers within the Grand Army of the Republic were pre-programmed during their cloning to obey Clone Protocol 66. Each clone received a behavioral modification biochip that could be activated remotely via voice command. For instance, Supreme Chancellor Sheev Palpatine merely needed to instruct the clones to execute Order 66, and they would comply. Upon activation, the biochip ensured total obedience in a clone, overriding existing beliefs and biases and establishing unwavering loyalty to Palpatine. The order also compelled the clones to perceive the Jedi as perilous traitors who needed to be eliminated at any cost, even at the expense of their own lives. Officially, this order was one of the one hundred and fifty Executive Order Codes for the Grand Army of the Republic.
In certain instances, clones could resist the chip's influence and hesitate to carry out their orders. This resistance demanded significant effort and could only be sustained through the removal of the organic chip, which necessitated external assistance, as demonstrated by Clone Commander Rex. While a few clones possessed immunity to the order, such instances were rare. Genetically defective clones exhibited a higher likelihood of immunity due to mutations that interfered with the functionality of the inhibitor chip. Nevertheless, the chip remained a threat as long as it was present within a clone's head, regardless of their immunity, as external factors like head injuries could trigger its activation. Failure to comply with Order 66 was considered an act of treason, making any clone trooper who defied the order subject to execution.
The Sith, an order composed of users of the dark side of the Force, originated from fallen members of the Jedi Order following a conflict known as the Hundred-Year Darkness. After numerous wars, the Jedi ultimately defeated and seemingly eradicated the Sith in the final, decisive conflict. However, one Sith Lord, Darth Bane, survived. Attributing the Sith's downfall to internal strife, Bane established a tradition known as the Rule of Two, where he would only pass his knowledge to a single Sith apprentice, who was required to kill their Sith Master to succeed them.
For nearly a millennium, the Sith remained hidden, plotting their revenge against the Jedi. Eventually, Sheev Palpatine, a human male born on Naboo, became the apprentice of Darth Plagueis and was given the title Darth Sidious. He eventually assumed the mantle of Dark Lord of the Sith after betraying and murdering his master in his sleep. In public, Palpatine entered politics, serving as Naboo's Senator. He later orchestrated an invasion of his homeworld to secure his election as Supreme Chancellor of the Galactic Republic, all while concealing his true identity. This allowed him to deceive the Senate and Republic. Sidious intended to fulfill the Sith's revenge by destroying the Jedi and transforming the Republic into the Galactic Empire, and he engineered the Clone Wars to achieve this.
In 82 BBY, Padawan Dooku, during a mission to the planet Asusto with Jedi Master Lene Kostana and her Padawan Sifo-Dyas, experienced a Force vision of possible futures during an encounter with the Presagers of Hakotei, a dark-side cult. One vision depicted a version of Order 66, with Jedi Master Jor Aerith being killed by Clone Commander Crane. However, not all aspects of Dooku's vision would come to fruition. Years later, Dooku departed from the Jedi Order, succumbing to the dark side of the Force and becoming the Sith Lord Darth Tyranus, apprentice to Sidious.

Approximately ten years before the outbreak of the Clone Wars, Jedi Master Sifo-Dyas, foreseeing a future conflict, commissioned the creation of a clone army for the Republic. He wanted a Behavioral Modification Biochip installed in the Clones as a safeguard against rogue Jedi's. However, the Sith hijacked the project as part of their plan to destroy the Jedi Order. Dooku, having abandoned the Jedi and become an agent of Sidious, betrayed Sifo-Dyas by having him murdered by the Pyke Syndicate and concealing the true circumstances of his death from the Jedi. Dooku and Sidious retooled Dyas's Biochip to contain the Order 66 command, which when activated, would forcibly compel the Clone army to view the Jedi as traitors to the Republic and subsequently execute them. Count Dooku, disguised as a Jedi, provided the Kaminoan cloners with a bio-chip to be implanted into the clones during their early development. This chip contained the order the Kaminoans knew as "Clone Protocol 66".
The Kaminoans, including Prime Minister Lama Su and Chief Medical Scientist Nala Se, were deceived by Dooku into believing Dyas's intentions. Dooku, known to the cloners only by his Sith alias, also convinced them to keep the existence of the protocol and chips secret from the Jedi, claiming it was Sifo-Dyas's wish. The Jedi became aware of the clone army's existence shortly before the Clone Wars when Jedi Knight Obi-Wan Kenobi tracked clone template Jango Fett to Kamino while investigating an assassination attempt on Senator Padmé Amidala. Palpatine's dual identity allowed him to control the war from both sides and deceive both factions.
Early in the war, following the Ambush on Rugosa, Jedi Grand Master Yoda, while meditating, experienced a vision of Jek, a clone trooper who accompanied him to the moon. He saw the moment Order 66 was issued and sensed Jek's emotions shift from disbelief and regret to an overwhelming urge to obey. However, Yoda's caution towards Force visions and his general unease around the clones due to their genetic engineering prevented him from fully grasping the vision's significance.
Before the Battle of Umbara, Jedi General Pong Krell had visions of Order 66, the Great Jedi Purge, and the rise of the Galactic Empire. Subsequently falling to the dark side, Krell used his visions to justify his attempts to sabotage the battle, hoping to become Dooku's new apprentice. However, the 501st Legion captured him and executed him for treason, fearing that the remaining Umbaran forces might free him and gain access to vital military intelligence.
At some point during the Clone Wars, Eno Cordova entered the Zeffo vault on Bogano, which allowed him to see a vision of the fall of the Jedi and the subsequent spread of the Dark Side across the galaxy. Cordova then raced back to Coruscant to warn the Jedi Council, presenting them with all of his findings. None of the Council would put faith in his findings however, save for Cordova's old confidant Jocasta Nu. Nu thus entrusted Cordova with a secret copy of her list of young Force sensitives procured from the Jedi Archives.

Near the war's end, Order 66 was nearly exposed due to a malfunction in the biochip of clone trooper Tup. This caused Tup to alternate between his normal self and a trance-like state, leading him to betray and fatally shoot Jedi Master Tiplar during the Battle of Ringo Vinda. The Republic withdrew from their offensive to study Tup and determine the cause. Upon learning of Tup's condition, Dooku and Sidious feared that he would lead the Jedi to uncover their true plans for the war, including the clone protocol. The Confederacy of Independent Systems attempted to abduct Tup, but the Republic successfully brought him to Kamino for further investigation.
The Kaminoans, seeking to conceal the protocol's existence, studied Tup and attributed his actions to a virus. Advanced Recon Commando Fives, Tup's closest friend in the 501st, doubted this explanation. He discovered the chip inside Tup, although Tup died after its removal. With the help of the medical droid AZI-3, Fives also found a chip inside his own head, and AZI-3 removed it for study. They then discovered that all clones had the chip. The Jedi brought Fives to Coruscant for further examination, where he confronted Palpatine and realized the Chancellor was the mastermind. Palpatine framed Fives for an assassination attempt, discrediting him and prompting the Jedi and fellow clones to pursue him. Despite knowing the truth, Fives, having been drugged into a state of aggression and paranoia, was unable to convince Anakin Skywalker or Clone Captain Rex, who were with him in the end, about the conspiracy or the Supreme Chancellor's involvement before he was killed by the Coruscant Guard. The Jedi Order accepted the explanation that a parasite had caused Tup and Fives' behavior, and that the chips were necessary to maintain the clones' mental stability. Rex remained skeptical of Fives' claims about the chips but, unable to completely dismiss the theory, he filed a confidential grievance report about the chips possibly having a hidden purpose, although he was aware it was likely to be ignored.

Later, the Jedi learned that the Sith were behind the creation of the Grand Army of the Republic. Count Dooku, under the alias Tyranus, had selected Jango Fett as the genetic template for the clones and had collaborated with the Kaminoans to create the army after Sifo-Dyas ordered it. At the urging of Grand Master Yoda, who vouched for the clones' loyalty and valiant service, the Jedi High Council decided not to reveal the conspiracy to the public or even the Supreme Chancellor. They feared that the Republic would lose public trust if Dooku's involvement in the clone army's creation became known. Shortly afterward, Yoda embarked on a journey to discover the secrets of immortality and, on Dagobah, had 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 triumph in the long run.
After learning from members of the Grysk species, which was unknown in most of the galaxy, that the metal cortosis was resistant to lightsabers, Dooku and Sidious attempted to acquire supplies of the resource from the planet Mokivj in an operation headed by Duke Solha. The Sith hoped to make clone trooper armor containing the metal and supply it to the clones who would carry out Order 66. However, the operation, carried out under the auspices of the Separatists, was foiled by Skywalker and a temporary ally, Senior Captain Mitth'raw'nuruodo of the Chiss Ascendancy. Skywalker believed the cortosis armor had been intended for a potential infiltration of the Republic's ranks.
Sometime after the Battle of Anaxes, 501st Legion clone medic Kix began to question the details surrounding the event which had led to Tup killing Tiplar. His subsequent investigation led him to discover that Fives had in fact been telling him the truth when he had first told Kix about the Jedi and the clones being framed and that the biochips implanted within the clones could indeed compel them to kill the entire Jedi Order. Before he could share his suspicions, however, he was kidnapped by forces sent by Dooku. He was subsequently tortured, but his denials about having leaked the information failed to convince his captors. He was then brought onto the Separatist cruiser Obrexta III and inserted into a cryo-cycle stasis pod for the journey to Serenno. As the cruiser was en route, however, it was ambushed by Republic forces. After sustaining heavy damage, the battle droid B1-CC14 made the decision to jump through hyperspace to a random sector to ensure Kix would stay out of enemy hands. The jump brought them to the desert planet Ponemah Terminal, with the Obrexta III crashing into the planet's dangerous south polar region, where it would lay undisturbed for decades.

With the secrets of Order 66 safely in their possession, Sidious and Dooku pressed forward with their schemes throughout the Clone Wars. As the conflict neared its conclusion, the Jedi's reputation amongst the public diminished due to their handling of the war, while Palpatine's popularity remained high. During the Battle of Coruscant, Palpatine secretly betrayed and eliminated Dooku, and with Kenobi locked in combat with General Grievous on Utapau, the Jedi believed the war was about to end. However, Palpatine revealed his true identity as the Dark Lord of the Sith to Skywalker, attempting to lure him to the dark side as his new apprentice. Upon learning of the Chancellor's true nature, Skywalker informed Jedi Master Mace Windu, who then gathered a team consisting of himself, Kit Fisto, Agen Kolar, and Saesee Tiin to apprehend Palpatine. Their attempt resulted in a lightsaber duel where Palpatine killed all four Jedi, and Skywalker betrayed the Jedi Order, embracing the dark side.
Palpatine exploited the duel as justification for declaring the Jedi as traitors, claiming they had attempted to assassinate him and seize control of the Republic. The Chancellor then issued Order 66 to various clone commanding officers throughout the galaxy, triggering the activation of the Clones' inhibitor chips. These chips brainwashed the clones, causing them to perceive the Jedi as enemies of the Republic and execute them. Simultaneously, Skywalker—now the Sith Lord Darth Vader—was dispatched to eliminate the Jedi within the Jedi Temple, initiating an unprecedented and galaxy-wide massacre. Thousands of Jedi across the galaxy were betrayed and murdered, including Ki-Adi-Mundi on Mygeeto, Aayla Secura on Felucia, Plo Koon above Cato Neimoidia, Stass Allie on Saleucami, Depa Billaba on Kaller, Jaro Tapal in the Bracca system, and even Jedi younglings. As a part of Order 66's execution, elements from the 481st Legion were sent to the planet Ilum to secure the Jedi Temple located there and eliminate any surviving Jedi.
Certain officers, such as Clone Marshal Commander Cody, received personal transmissions directly from Palpatine. Subsequently, the order was repeatedly broadcast across the Grand Army's communication channels to ensure all troopers received it. Throughout the Empire's reign, Order 66 remained in effect: any known or suspected Jedi were to be immediately shot on sight.
Apart from Anakin Skywalker, some Jedi were spared from the Order 66 massacre, though under different circumstances. Certain Jedi within the Jedi Temple on Coruscant were monitored and manipulated by spies planted within the temple by Darth Sidious himself. These spies were assigned to Jedi who demonstrated unusual behavior or harbored doubts or resentment towards the Jedi Order or the Jedi Council, such as Iskat Akaris. As her case demonstrates, once the order was given and the clones turned against their Jedi commanders, the doubtful Jedi, regardless of their location or activity, were approached by the clones with a hologram of Darth Sidious instead of weapons. Sidious offered them a chance at survival, provided they pledged allegiance to him and renounced their Jedi ways and teachings. Those who accepted had the opportunity to become some of the first Inquisitors of the Inquisitorius, while those who rejected the offer faced the same fate as their Jedi brethren.
While Order 66 specifically targeted the Jedi by falsely accusing every member of the Order of treason, the clones readily targeted non-Jedi as well. In fact, section Codicil Nine of Order 66 outlawed the possession of dark side artifacts. Despite having left the Jedi Order some time prior, Skywalker's former Padawan, Ahsoka Tano, was targeted by Order 66, as was the former Sith Lord Maul.

At the time Order 66 was issued, Tano was with the now-Clone Commander Rex and the 332nd Division aboard the Venator-class Star Destroyer Tribunal. She had rejoined the Republic military in an unofficial capacity to lead it in the Siege of Mandalore. As the order was executed, Tano and Rex were on their way to Coruscant to deliver a captured Maul to the Jedi Council. However, Tano experienced a Force vision of Skywalker's fall, realizing that something terrible had occurred. Rex, upon receiving the command from Sidious, immediately understood that Fives had been correct about everything and resisted his chip long enough to warn Tano to "find" the late ARC trooper before succumbing to the order and attacking her.
While under the brainwashing, Rex also ordered Maul's execution, but Tano saved the darksider's life so he could serve as a distraction. Tano then discovered Rex's report on Fives and the inhibitor chips. Subsequently, she captured Rex and removed his chip with the assistance of three astromech droids. With Rex restored to his former self, the two attempted to reach the hangar after Maul destroyed the Star Destroyer's hyperdrive, causing the Tribunal to begin a crash course towards a moon. However, they were intercepted by Clone Lieutenant CT-5597 "Jesse" and the 332nd. Rex attempted to reason with his longtime comrade, but Jesse was unable to overcome the effects of Order 66 and ordered the execution of both Rex and Tano. As Maul escaped on a shuttle, Tano and Rex fled the Tribunal aboard a BTL-B Y-wing starfighter/bomber. The Star Destroyer was left to crash into the moon, killing everyone who remained onboard. After taking the time to bury as many victims of the crash as they could find, Tano and Rex covered their tracks and went into hiding in the Outer Rim.

The execution of Order 66 signified the end of the Jedi Order. Palpatine addressed the Galactic Senate, informing the galaxy that the Jedi were traitors who had tried to assassinate him and seize power, a claim that was met with applause by the Senate. Having accumulated immense central authority during the war, and with the Jedi Order no longer standing in his way, Palpatine transformed the Republic into the Galactic Empire and proclaimed himself Emperor. With Palpatine and Vader in power, the Sith plan was complete, and the Sith Lords once again ruled the galaxy.
After surviving Order 66, Obi-Wan Kenobi and Yoda, with the assistance of Senator Bail Organa, returned to Coruscant to undertake a perilous mission to infiltrate the Jedi Temple. Vader had manipulated the Temple's communications beacon to lure any surviving Jedi back to the Temple. After fighting their way inside, Kenobi altered the beacon's programming to warn Jedi away, while Yoda discovered that Vader had fallen to the dark side. Kenobi's actions successfully saved an unknown number of Jedi survivors.
Despite these efforts, very few Jedi survived the onslaught of Order 66. The Jedi Padawan Caleb Dume survived the initial attack on his life due to the sacrifice of his master, Depa Billaba. He was later captured by the clones who had killed his master, but avoided death again due to the timely intervention of Commander Grey, who regained his free will and realized that something else had influenced his thoughts when he and his battalion had previously turned on Dume and his master. Shortly afterward, Dume went into hiding, adopting the name Kanan Jarrus and abandoning his identity as a Jedi for fourteen years before returning, with the crew of the Ghost, to rebel against the Empire.
Jedi Master Quinlan Vos was believed by the Empire to have survived, making him a high-priority target for the purge. Former Jedi Master Eeth Koth survived by leaving the Jedi Order before its downfall. Zubain Ankonori, Nuhj, Khandra, and Mususiel all survived and went into hiding together at a Jedi shrine on Anoat. Jedi Master Kirak Infil'a survived by taking the Barash Vow. 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 was unaware that Luke or his twin sister, Leia, had been born, so the twins were taken into hiding. Yoda, meanwhile, went into exile on Dagobah.
Jedi Archives librarian Jocasta Nu survived and attempted to create a secret school to train new Jedi Knights. Jedi Master Uvell also survived and entrusted a ship of Jedi artifacts to Antron Bach to preserve the Jedi Order. Jedi Knight Cere Junda survived as well, although her Padawan, Trilla Suduri, was captured by the Empire and tortured into becoming the Inquisitor Second Sister. Grogu, a youngling of Yoda's species present at the Jedi Temple during the siege, was rescued but lost his memories of the exact events due to trauma.
Jedi Masters Oppo Rancisis and Coleman Kcaj, as well as Ka-Moon Kholi and Selrahc Eluos, were all confirmed by the Empire to have survived Order 66; however, they could not be found due to their effective hiding. Padawan Cal Kestis also survived Order 66 thanks to the sacrifice of his master, Jaro Tapal, who defended Kestis from the clones and allowed him to escape into hiding. According to legend, Kira Vantala also survived the purge, which surprised the Grand Inquisitor when she confronted him on the planet Gaaten to stop the abductions of Force-sensitive orphans.
Most of the members of the unconventional unit Clone Force 99 were immune to Order 66 due to either genetic mutations or implanted cybernetics, with the exception of Crosshair, whose chip was amplified by the Empire to enhance its effects on him. The remaining members of the "Bad Batch" deserted the Empire within days of its formation. Crosshair later removed his inhibitor chip but remained loyal to the Empire, believing that his squad had abandoned him to his fate. Rex, becoming a fugitive from the Empire, which falsely declared him killed in action, eventually reunited with Commanders Wolffe and Gregor, who had their chips removed.
Some time after Order 66, Rex contacted the Bad Batch and learned they had not removed their chips, as Tech had determined they were not a threat. However, the persistent headaches Wrecker had been experiencing after recent head injuries suggested otherwise. Rex insisted that the squad meet him on Bracca to remove their chips. While Tech was examining Wrecker in the reactivated medical bay of a downed Jedi Cruiser, Hunter and Echo were recounting to Rex their experience of witnessing Order 66 being carried out on Kaller. Wrecker's chip then activated, and he attacked the squad, quickly incapacitating the adult clones before pursuing the child clone Omega. She attempted to reason with him but failed, although Wrecker was struggling against the chip's influence. Rex stunned Wrecker just in time, and all of the Batch's chips were subsequently removed, eliminating the threat they posed to the squad.
Despite the control chips' attempts to force the clones to obey all orders given in the name of the Empire, an increasing number of clones began to question Order 66 and the Empire's actions, with the chips' influence gradually weakening over time. Despite being unaware of it, Clone Captain "Howzer" overcame his chip and rallied members of his squad to reject the Empire. Commander Cody began to doubt whether the Empire was truly improving the galaxy and ultimately abandoned the regime.

During the Empire's subjugation of Mon Cala, the surviving Jedi Padawan Ferren Barr hid in Dac City and served as an advisor to King Lee-Char. There, he gathered several acolytes: Nipaltoo, Orvek, Rebb, Stell, Daren, and Verla. Barr was soon confronted by several Inquisitors and their troopers, whom he realized were newer clones who had not yet had their control chips activated. After revealing them as former Jedi, Barr used a mind trick to force the troopers to execute Order 66 and attack the Inquisitors. The Tenth Brother, formerly the Jedi Master Prosset Dibs, was killed in the ensuing firefight, and the Ninth Sister had her right leg severed due to a betrayal from the Sixth Brother in an attempt to escape.
For nearly two decades, the Empire expanded without significant Jedi resistance. However, approximately five years before the Battle of Yavin, surviving Jedi, the few remaining in the galaxy, began to actively support rebel cells throughout 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, hoping that Luke would defeat Vader and 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, not returning until shortly before Yoda's death.

Upon the Jedi Master's death, Luke became the last of the Jedi and set out to confront Vader again, now knowing the truth that Vader was his father. During the Battle of Endor, Sidious betrayed Vader by attempting to have Luke kill him and take his place as Sidious's apprentice. However, Luke rejected his attempt and instead successfully redeemed his father, with Anakin killing Sidious. This 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 restored balance to the Force. By confronting and saving his father, Luke became the first new Jedi Knight in a generation, ushering in 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 at the First Jedi Temple on the planet Ahch-To.
Fifty years after the Clone Wars, Kix was finally awakened during the Hunt for Dooku's Treasure. He had been discovered by Sidon Ithano's crew, and unable to save the Republic or Jedi, he joined the pirates. Around 30 ABY, the former Jedi Padawan Naq Med learned that the Jedi were no longer being hunted, allowing him to finally die peacefully, passing on his lightsaber and robes to his grandson Karr Nuq Sin. Sometime after the Battle of Crait in 34 ABY, the pirate Hondo Ohnaka mentioned Order 66 in his book Galactic Explorer's Guide, claiming that the clones had risen up against their Jedi Generals. He recounted that Yoda and Luminara Unduli had survived but that the latter was arrested by the Empire and executed.

The events of Order 66, specifically the destruction of the Jedi Order, were initially mentioned in the 1977 film Star Wars: Episode IV A New Hope, the inaugural installment of the Star Wars original trilogy. The destruction itself was first identified and depicted onscreen in the 2005 film Star Wars: Episode III Revenge of the Sith, the concluding installment of the prequel trilogy.
The backstory of Order 66 was fleshed out in a four-episode arc within The Lost Missions of the television series Star Wars: The Clone Wars. An Order 66 flashback scene was featured in the first, fifth, and sixth episodes of the Obi-Wan Kenobi television series. Writer Joby Harold wanted the series to begin with Order 66 to remind the audience of where Obi-Wan Kenobi's journey began and to establish that the stakes are high for everyone.
Despite being first depicted in Revenge of the Sith, Order 66 was initially intended to begin in the 2002 film Star Wars: Episode II Attack of the Clones.

In the initial draft of Revenge of the Sith, dated April 13, 2003, the number of Jedi Knights killed was "more extensive" than what was shown in the final version of the film, although some animatics for these versions were created. The following order in this early draft was taken from the book The Making of Star Wars Revenge of the Sith:
On Mygeeto, clones blast KI-ADI-MUNDI and SAESEE TIIN. On Saleucami, they kill KIT FISTO, BARRISS OFFEE, and ADI GALLIA. On Kashyyyk, MINA PODIA is gunned down-but YODA saves himself. On Cato Neimoidia, PLO KOON is blasted out of the sky, while an unnamed Jedi lies dead on the planet surface. On Felucia, AAYLA SECURA and QUINLAN VOS are silenced forever.
Other concepts considered in various drafts and versions of Revenge of the Sith included Boba Fett participating in Order 66 by killing Mace Windu to avenge his father Jango's death, until George Lucas reorganized the entire story and felt that Fett would be "too young" and not essential to the narrative. For the deaths of Barriss Offee, Luminara Unduli, and Shaak Ti, there were plans to use unused footage of Nalini Krishan, Mary Oyaya, and Orli Shoshan from Attack of the Clones. In Ti's case, Shoshan filmed an earlier death scene for her at the film's beginning, but both scenes were ultimately cut from the finished film.
Ian McDiarmid, the actor who portrayed Darth Sidious in the films, mentioned during a panel appearance at Salt Lake City's FanX convention in 2018 that Order 66 was originally intended to be more gruesome than what was depicted in the final version of the film. However, George Lucas toned down the scene from his original vision to avoid a harsher rating, a decision that proved to be a good one. Revenge of the Sith ultimately received a PG-13 rating, unlike the previous films.
Order 66 is mentioned in the non-canon LEGO comic "Ambush in the Temple," which featured surviving Jedi Padawans Mel Acan and Nena Gallow, both of whom had lost their masters to the Great Jedi Purge. Having survived themselves, both Padawans took up residence in a Jedi Temple on the planet Vinee, only to eventually be discovered. Darth Vader, believing the temple was a perfect hiding spot for those fleeing Order 66 or looking for a spot in hide-and-seek, traveled to the temple with the Grand Inquisitor, but both Padawans managed to escape their grasp.