- "Execute Order 66."
- ―Darth Sidious to numerous 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 trained to obey without hesitation. The order branded members of the Jedi Order as traitors to the Republic and called for their immediate execution without question. The issuing of the order by Supreme Chancellor Palpatine marked the formal beginning of the Great Jedi Purge, and signified the rise of the Galactic Empire. It was chief among the atrocities that led to 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 the acts of surviving Jedi, such as Obi-Wan Kenobi and Yoda, teaching Luke Skywalker the ways of the Force.
- "Statement: Overwhelming odds is also a good tactic, master. There are few Jedi that can long hold their ground against a hundred attackers all firing at once… or being turned on by their own troops."
Prelude to Order 66
- "I sense a plot to destroy the Jedi. The dark side of the Force surrounds the Chancellor."
- ―Mace Windu
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 Grand Army of the Republic (GAR) were prepared to execute, immediately and without question, and only in specific cases of extreme necessity. It was originally designed as a fail-safe by Jedi Master Sifo-Dyas against rogue Jedi. 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. In particular, Order 65 dealt with the detention and possible execution of the Supreme Chancellor by the Republic if he became unfit for office, further hiding the true intention of Order 66. 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. The text of the order ran:
|Source: Republic Commando: True Colors||Attribution: Karen Traviss|
Order 66: In the event of Jedi officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander (Chancellor), GAR commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established.
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Under close examination, the text of Order 66 exposed several distinctions that set it apart from the other contingency orders. First, the majority of the other known contingency orders took into account other sources of command authority—the Vice Chair Mas Amedda, the Senate Security Committee, the Jedi Council, the GAR High Command—while Order 66 could only be issued by the GAR Supreme Commander—in this case, Palpatine. Second, it was not required that the Security Council or a Senate majority declare that the Jedi were acting against Republic interests; Palpatine alone had the power to make that determination. Third, GAR commanders were not required to authenticate the order, or even to report it to any other command authority. If the order came directly from Palpatine, using specific command phrasing and over specific communications channels pre-approved by him for this express purpose, that was all the authentication the clone commanders appear to have needed. Fourth, there was no apparent mechanism for rescinding the order. Once given, it had to be followed.
Finally, there was no proviso—as there was in other known contingency orders—that the Jedi were to be detained and that lethal force should be used if necessary; the order explicitly specified that they were to be removed by lethal force. Though the true purpose of this specific command was to satisfy Darth Sidious's wish to eliminate the Jedi as a threat to his power, the insistence on lethal force could have been rationalized on general—that is, non-Sith—grounds: it could be argued that any attempt to detain a Jedi who did not wish to be detained would fail, except in the event that said Jedi was faced with overwhelming GAR numbers, and even then, such an attempt would likely result in numerous unnecessary GAR casualties. The use of lethal force would therefore be considered necessary to preserve the lives of GAR soldiers and officers.
In order to test out Order 66, Order 99 was programmed into the Separatist Droid Army, being issued to B1-Series battle droid "Coppertop" during the Battle of Bogoa. To further ensure that various clone troopers carried out the plan when the time came, the order was programmed into a biochip implanted into their brains during development.
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 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 Tyranus, otherwise known as Count Dooku, learned of this from Admiral Trench, and planned to have Tup abducted during transport to Kamino to investigate his erratic behavior, realizing that his current status would 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 managed to retrieve Tup, although this also resulted in the former uncovering the order and thus the conspiracy. Fives was later killed by Fox 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 Palpatine 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 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 death 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 quickly cut down 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 pretext necessary to enact Order 66.
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 Skywalker's emotional distress and pressured him to turn to the dark side of the Force. Unsure what to do and feeling he could never be forgiven for what he had done, as well as 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
- "It will be done, my Lord."
- ―Commander Gree complies with 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 issued Order 66. He employed a channel that made the authenticity of the order unquestionable, but ironically, the signal was encrypted using a Separatist code—one of the rare clues that he was, in fact, the hidden hand behind both sides of the war.
Palpatine sent word 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, almost every one 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 harbored 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, shot down by Captain Jag; Stass Allie on Saleucami, at the hands of Commander Neyo and CT-3423; Aayla Secura on Felucia fell to Commander Bly and members of the 327th Star Corps; and Ki-Adi-Mundi on Mygeeto, who managed to deflect a few shots before being overwhelmed 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 upon him, but Kenobi managed to survive and escape the planet. He soon reunited with Grand Master Yoda, who had also escaped a sneak attack by Commander Gree and a second clone trooper on Kashyyyk, beheading both clone commander and trooper in the process.
Although Order 66 was only issued to the Grand Army of the Republic, a MagnaGuard droid on Utapau implied upon being reactivated that a similar order to destroy all Jedi was implemented for at least that droid.
Not all clone troopers obeyed the Order, however. On Murkhana, Roan Shryne and Olee Starstone were rescued from Order 66 by members of Ion Team. 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 feigned 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
- "I saw thousands of troops attack the Jedi Temple. That's why I went looking for Yoda."
- ―Bail Organa
On Coruscant, Senate Emergency Response announced a state of martial law over the planet, 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. No Jedi within the building were spared, but some escaped, including Shaak Ti, Sha Koon, Kazdan Paratus and Jin-Lo Rayce.
- "Would it have been too much to ask for the order to have come through before I gave him back the bloody lightsaber?"
- ―Commander Cody, speaking of Obi-Wan Kenobi, after receiving Order 66
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 and claimed the lives of many of the survivors of the initial onslaught. Nearly all the surviving Jedi Knights were hunted down and killed by Darth Vader, while Order 66 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 eluded Imperial forces for many years, a feat few of their contemporaries could claim.
- "Every single Jedi, including your friend, Obi-Wan Kenobi, is now an enemy of the Republic."
- ―Darth Sidious to Darth Vader
The majority of the Jedi across the galaxy fell victim to Order 66. Specifically targeted were the leaders of the Order: the Jedi Council. Masters were to be immediately executed, Knights detained or executed, and Padawans detained for interrogation.
- Master Ali-Alann: Stationed at the Jedi Temple; killed by the 501st Legion.
- Master Stass Allie: Stationed on Saleucami; killed by Commander Neyo and CT-3423.
- Jedi Battlemaster Cin Drallig: Stationed at the Jedi Temple; killed by Darth Vader.
- Master Sian Jeisel: Visiting the Bogden Jedi chapter house; killed herself and several clone troopers.
- Gate Master Jurokk: Stationed at the Jedi Temple; killed by Darth Vader.
- Master Ki-Adi-Mundi: Stationed on Mygeeto; killed by Commander Bacara and the Galactic Marines.
- Master Plo Koon: Stationed on Cato Neimoidia; killed by Captain Jag.
- Master Ferroda: Stationed on Cato Neimoidia; killed by X2.
- Master Saras Loorne: Stationed on Murkhana; killed by the 22nd Air Combat Wing.
- Master Du Mahn: Stationed at the Bogden Jedi chapter house; killed by clone troopers.
- Chief Archivist Jocasta Nu: Stationed at the Jedi Temple; killed by Darth Vader.
- Master Simms: Stationed on Toola; killed by Commander Keller.
- Master Sev: Stationed above Ragmar V; killed by clone troopers.
- Master Traavis: Stationed on Garqi; killed by Sarge.
- Master Luminara Unduli: Stationed on Kashyyyk; killed by Commander Faie.
- A group of Masters: Stationed at the Jedi Temple; killed by Darth Vader.
- The master who protected the Great Holocron: Stationed at the Jedi Temple; killed by Darth Vader.
- A Zabrak Knight: Stationed at the Jedi Temple; killed by Darth Vader.
- Knight Nem Bees: Stationed on Orto; killed by Commander Deviss.
- Knight Aayla Secura: Stationed on Felucia; killed by Commander Bly and members of the 327th Star Corps.
- Knight Olana Chion: Stationed at the Jedi Temple; killed by the 501st Legion.
- Knight Serra Keto: Stationed at the Jedi Temple; killed by Darth Vader.
- Knight Barriss Offee: Stationed on Felucia; killed by Lieutenant Galle.
- Knight Etain Tur-Mukan: Stationed on Coruscant; killed indirectly by another Jedi while protecting a clone trooper.
- Knight Tru Veld: Stationed at the Jedi Temple; killed by the 501st Legion.
- Two Unidentified Knights: Stationed on Murkhana; killed by clone troopers.
- Between 3 and 7 Padawans (2 boys, one girl and 4 unspecified Jedi): Trying to escape Coruscant, they were discovered by a checkpoint of the 501st and died in the melee. One of them accidentally killed Jedi Knight Etain Tur-Mukan in the melee.
- Padawan Bene: Stationed at the Jedi Temple; killed by Darth Vader.
- Padawan Zett Jukassa: Stationed at the Jedi Temple; killed by Sergeant Fox and members of the 501st Legion.
- Padawan Whie Malreaux: Stationed at the Jedi Temple; killed by Darth Vader.
- Youngling Sors Bandeam: Stationed at the Jedi Temple; killed by Darth Vader.
- Youngling Jeswi Ele: Stationed at the Jedi Temple; killed by Darth Vader.
- Youngling Shia Letap: Stationed at the Jedi Temple; killed by Darth Vader.
- Unidentified Clan: At least several more younglings hiding in the High Council Tower.
- Several members of the Soaring Hawkbat Clan: Stationed at the Bogden Jedi chapter house; killed by clone troopers.
- Hundreds of other Jedi
It was said that fewer than one hundred Jedi—approximately one percent of the entire Order—survived Order 66. However, the number seemed closer to two hundred. The anti-Jedi sentiment that Palpatine had fostered during the Clone Wars and the false reports of an attempted Jedi coup had branded the Jedi as warmongering traitors. Hated by the galaxy at large and unable to challenge Palpatine's new government directly, these survivors were forced into hiding. Many of them were hunted down and killed over the next two decades by Vader and his agents.
Initially, four Jedi on Dellalt escaped with their lives: Klossi Anno, Deran Nalual, Siadem Forte, and Iwo Kulka. A group that was fighting on Murkhana were saved by their troops but one of their number, Bol Chatak, was later killed by Vader. The other Jedi, Roan Shryne and Olee Starstone, then fled, meeting up with the group fleeing Dellalt. Forte and Kulka died at Darth Vader's hands, along with Shryne, while the others escaped to attempt to attack the Empire on smaller fronts. A group of several Jedi combatants in the Battle of Shumari, except for the young Tao, were all hunted down by the Sith. Dass Jennir led his own fight against the Sith along with a group of rebels, while fellow Jedi Kai Hudorra and Noirah Na went into Imperial City to try and become "normal" citizens. Kai Justiss attempted to hide from bounty hunters. Ekria, Zonder, and Drake Lo'gaan escaped Felucia alive, though Zonder died in a duel against Vader. Chase Piru watched after younglings from the Soaring Hawkbat Clan, including Seddwia, Jiro, and Kennan Taanzer. Tholme died at some point and had a funeral pyre on Anzat. Beyghor Sahdett slaughtered the clones that attacked him, and a female Jedi was able to hide from her clones.
Obi-Wan Kenobi, Yoda, and Shaak Ti were the only High Council members to survive the initial purge. Maris Brood survived and went into hiding along with Shaak Ti on Felucia, while Kento Marek hid amongst the Wookiees on Kashyyyk. Aven Rolk survived, as he was frozen in stasis for decades in an escape pod, and planned to rebuild the Jedi Order but later died in an ice cave on the planet Zissh.
Celeste Morne escaped the initial order as she had slept in an Oubliette since the Mandalorian Wars. She later was awakened by Darth Vader on board the smuggling vessel Uhumele. She survived her confrontation with Vader, but died nearly a hundred years later at the hands of Cade Skywalker, in an act of mercy, on Had Abbadon.
At a meeting on Kessel, the Sith executed Koffi Arana, Tsui Choi, Roblio Darté, Jastus Farr, Ma'kis'shaalas, Shadday Potkin, Bultar Swan, and Sia-Lan Wezz. Morvet Storm was killed soon after, when Vader attacked his home; however, his son escaped Vader.
Aqinos and his Iron Knights hid on Dweem, while Lady Caryn took a Padawan, Ana Tathis, and then fled into the Unknown Regions. While Ana Tathis eventually joined the Rebel Alliance, Caryn's final fate remained unknown. Minos Fel'Kona and his father, Jonas Fel'Kona, fled the devastated Cularin system and disappeared. Geith Eris, Callista Ming, and Plett hid on Belsavis away from the fighting though were eventually found. However, Plett escaped and established a sanctuary on Belsavis for other surviving Jedi. Bon and Nia were found by a traveler and escaped the Purge. Darrus Jeht tricked his clone troops and fled to parts unknown. Ylenic It'kla later died on Alderaan during its destruction, while Bardan Jusik fled to Mandalore. Drakka Judarrl, Bre'ano Umakk and her master hid on Dantooine, Matarmeno Krahnn was exiled to Corellia, Antaria Wellos remained on Rori well into the time of the Galactic Civil War, and Quinlan Vos presumably hid on Kashyyyk with Khaleen Hentz and their son, Korto Vos. Tallisibeth Enwandung-Esterhazy, Arligan Zey, Kina Ha and Bardan Jusik survived and were brought to Mandalore by Nyreen Vollen. Jedi Master Hylon and his apprentice, Dendro, were cut down by Vader during a fierce clash on Otavon XII.
Darrin Arkanian was killed by High Inquisitor Antinnis Tremayne, but his apprentice, Corwin Shelvay, escaped. To escape a similar fate, Neth Enasteri left his family and fled into the Outer Rim. Ydra Kilwallen and her husband lived in peace for several years until they were lost to the Ssi-ruu. Niebur Boton, Dama Montalvo, a Gotal Jedi, and Halagad Ventor were tortured by Vader, with Ventor giving the locations of several surviving Jedi, along with his friend Ashka Boda's hiding spot. While Boton was tortured to death and mutilated by Vader, Ventor was released and went insane because of the deaths he had caused, though he was eventually redeemed. Ameesa Darys was killed by Arden Lyn, while the Last Curator of Records, Aidan Bok, Axton Tredway (though some of Tredway's relatives survived), and another Jedi on Talasea was hunted and killed by the Sith Lord.
Kaoln, Rorr'hn, Gruu Dunrik, Drun Cairnwick, Dorn Tavers, Tyneir Renz, Rachi Sitra, Fable Astin, Qu Rahn, Echuu Shen-Jon, Rahm Kota, Fable Astin, Corwin Shelvay, Drakka Judarrl, Ana Tathis, and Ylenic It'kla were some of the few remaining Jedi who had joined the Rebel Alliance and fought with the legendary Luke Skywalker against the Empire, though Ylenic perished during the destruction of Alderaan. A Jedi that was captured by the Empire led the Death Star Uprising, during which he was killed. Fable Astin and her mother joined the Alliance and helped combat the Empire. Ranik Solusar and his son were hunted, with Kam eventually joining the New Jedi Order. Qu Rahn was eventually slain by an Imperial Inquisitor shortly after the Battle of Endor. However, his spirit transcended the physical plane and would help Kyle Katarn in his quest for the Valley of the Jedi. Vima-Da-Boda hid in shame in the Outer Rim after the Order's fall. Echuu Shen-Jon had gone into hiding early into the Clone Wars on Krant, due to the fact he had fallen to the dark side. He later reemerged and saved Leia Organa from a squad of stormtroopers. He was later struck down by Vader after a fierce duel, but lived on as a Force spirit.
Vima-Da-Boba, Empatojayos Brand, T'ra Saa, K'Kruhk, as well as possible students of his, Nichos Marr, Aqinos, and most members of the Iron Knights, and Ephaan Kenzon, including some of his students, later joined Luke Skywalker's New Jedi Order. Brand had been severely injured by Vader during a dogfight near Ganathan Space during the Purge, but was rescued and outfitted with a cybernetic life support suit. He later sacrificed himself to help defeat a reborn Palpatine.
Ikrit went into a hibernation trance in 378 BBY on Yavin 4, remaining undiscovered during the Purge. He joined the New Jedi Order after awaking in 22 ABY, and died four years later during the Yuuzhan Vong War sacrificing himself to cover the escape of several other Jedi.
Beldorion, Jerec, Danaan Kerr, Maw, Travgen, Antinnis Tremayne, Dray, Quarmall, Sardoth, Jedgar and Sarcev Quest fell to the dark side and were eventually killed by other Jedi or Vader; Travgen was eventually redeemed. A'Sharad Hett eventually fell to the dark side, renamed himself Darth Krayt and created the One Sith; ironically becoming the main culprit for the Third Jedi Purge.
Shaak Ti, Rahm Kota, and Kazdan Paratus were all confronted by Darth Vader's secret apprentice, Galen Marek, during the Purge as part of the latter's training. Only Kota survived and apprenticed the young misled youth to the light, which led to Maris Brood's redemption. Kota went on to join the Rebel Alliance, and led the mission to capture the Death Star plans, despite his blindness. Jax Pavan and Laranth Tarak tried to undo the Empire on Coruscant. K'Kruhk eventually took a Padawan to the Hidden Temple.
Fy-Tor-Ana and Garen Muln hid on Ilum and were eventually killed when they met on the secret Jedi asteroid. Ry-Gaul was undercover during Order 66 but also fled to the Jedi asteroid, where he was killed. A Jedi attempt to attack a squad of clones at the Temple and was killed. Taj Junak sacrificed to save his academy and was killed by stormtroopers. Nos'lyn hid on Tatooine and helped Force-sensitives learn the ways of the Force. Qid Proko worked as a technician, and Urootar was killed on Kasshyyyk by a bounty hunter.
Jedi Master Falon Grey hid on Dantooine. During the Imperial Period, he led a rebellion against local Imperial stormtroopers. The elite clone trooper X2, having left Imperial service, helped Grey in the battle, but ultimately, X1 arrived and killed Grey.
Jedi Master Iri Camas was tracked by the 501st Legion on Celen. Luring a group of four clone commandos into the building, he ignited a gas line, causing the building to detonate. While three of the clones escaped, Camas and Bry were killed in the explosion; his lightsaber was later found half-melted in a wall opposite the explosion.
Valara Saar, Ood Bnar, Ferus Olin, Thracia Cho Leem, Codi Ty, and Zao were not active in the Jedi Order and therefore were not hunted by the Sith. Vergere was not in the galaxy at the time and was thus unaffected.
An'ya Kuro, an enigmatic and powerful Jedi Master, perished at Vader's hands in what Palpatine dubbed the final action of the Great Jedi Purge. A small group of Jedi Padawans survived the order by stowing away aboard a freighter.
Missing in action
There were many Jedi whose fate after Order 66 remained unknown. In the chaotic early days of the Empire, there were many reasons the fate of certain members of the Order remained unclear, chief among them being that either no body was 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, who was also believed to have been on Coruscant during Operation: Knightfall. Another missing Master was Eeth Koth, a former Council member. Obi-Wan Kenobi assumed that his longtime friend Bant Eerin was killed. Other Jedi whose fates were lost in the confusion were Joc Sah, Ahsoka Tano, Glynn-Beti, Ulu Ulix, Voolvif Monn, Pix, Saldith and Tera Sinube.
Behind the scenes
The first indirect mention of Order 66 was in the novelization of A New Hope, ghostwritten by Alan Dean Foster and published in 1976, which stated that the Jedi were "exterminated through treachery and deception."
In the first draft of Star Wars: Episode III Revenge of the Sith (April 13, 2003), the number of Jedi who were killed was "more extensive." The following excerpt from this draft is 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.
When Revenge of the Sith was released, some sources stated that Order 66 was preprogrammed into the clone troopers. However, George Lucas has stated that it was a "last resort" order, not preprogrammed. The order preceding Order 66 is Order 65, which stated that the Supreme Chancellor (had Palpatine not won the seat) would be removed from office by the GAR if the Galactic Senate declared him unfit for duty.
In the Star Wars: The Complete Saga Blu-ray set, the special-features disc shows the animation test for Order 66. It has more Jedi killed and different deaths for some. For example, Ki-Adi-Mundi is on a tower. An elevator then reaches the top with a large group of clone troopers inside, who kill him. Another example is Aayla Secura's death on Felucia with a large group of clones. They all kneel as droids pass ahead. Secura asks if they are droids. Bly simply says "no," and kills her. Another deleted scene from the film is set during Operation: Knightfall; Shaak Ti is shown meditating, and asks "What is it, Skywalker?" when Skywalker enters the room. Skywalker does not answer and simply stabs the Jedi Master.
It is unclear whether Order 66 was "programmed" into the clones or whether the Orders were taught to all clones. Karen Traviss's Republic Commando novels have mentioned that the Contingency Orders were taught and not programmed, resulting in several clones ignoring the order and/or refusing to go through with it outright, even "normal" (that is, a non-Commando, ARC, or any other special-forces clone) clones such as RC-5108/8843 "Corr." The novel Dark Lord: The Rise of Darth Vader also supports this, as Ion Team refused to execute the Order, and went rogue. In addition, George Lucas implied that the order was taught when explaining it was a last-resort order instead of pre-programmed. However, the sixth season of Star Wars: The Clone Wars revealed that the Contingency Orders are indeed planted in the minds of all clone troopers during their development via an organic biochip that subconsciously activates the Orders when given. This discrepancy is one of the many examples of Star Wars: The Clone Wars retconning established Legends material.