Infiltration of the Jedi Temple

In the year 19 BBY, the Grand Plan of the Sith to rule the galaxy and destroy the Jedi Order came to its long awaited fruition under the Sith Master Darth Sidious, who had controlled the Galactic Republic under his alter ego of Supreme Chancellor Sheev Palpatine and the Confederacy of Independent Systems through his pawns, including his Sith apprentice Darth Tyranus. After the Clone Wars between both factions raged for three years, Palpatine had achieved great executive powers, the Jedi Order's reputation was greatly damaged by the war, and many Jedi had been killed in combat. Additionally, the trust Jedi Knight Anakin Skywalker had in the Jedi High Council was damaged over the course of the war. Tempted to the dark side by Sidious's manipulations, the Sith Lord hoped to make Skywalker, who was believed to be the Order's Chosen One, into his new Sith apprentice when Tyranus was no longer needed. In particular, Skywalker's trust was heavily damaged when the Council turned its back on his Padawan Ahsoka Tano, who was left to be tried under the Republic Center for Military Operations until Skywalker discovered the true culprit, Padawan Barriss Offee. However, the experience persuaded Tano to leave the Jedi Order, leaving Skywalker to feel even more alone.

During the Outer Rim Sieges, the Jedi were dispatched across the Outer Rim Territories and elsewhere to lead the Republic Military against the Separatists in an effort to finally end the war, but the move actually served to further separate the Order's members from each other. After Tyranus was killed by Skywalker in the Battle of Coruscant, Sidious moved to corrupt Skywalker to the dark side as he experienced nightmares of his secret wife, Senator Padmé Amidala, dying in childbirth. As Skywalker's friend and former mentor Obi-Wan Kenobi engaged the current Separatist Head of State General Grievous in the Battle of Utapau, Sidious revealed his identity as a Sith to Skywalker. Although Skywalker quickly informed Jedi Master Mace Windu of the truth, Sidious's claims of being able to save Amidala tempted Skywalker enough that he chose to intervene in Windu's arrest attempt, culminating in Skywalker choosing the Sith Lord over his fellow Jedi by turning his lightsaber against Windu. Horrified over what he had just done, Skywalker agreed to Sidious's offer to become a Sith under the name "Darth Vader" on the condition that he could save his wife.

Told by Sidious that the Jedi were traitors and that the action would give him the power needed to save Amidala, Vader led thousands of clone troopers from his personal unit, the elite 501st Legion, into the Jedi Temple with the mission to wipe out all Jedi within, including the younglings. Using his authority as Supreme Chancellor, Sidious sent out the secret Clone Protocol 66 to the entire Republic Military across the galaxy, activating the behavioral modification biochips hidden within every clone and turning them against the Jedi they had served under. Vader and his forces were able to clear the entire Temple of opposition during Operation: Knightfall, targeting those who were children and adults alike, and light the building aflame.

While there were scattered pockets of survivors from Order 66, the galaxy was consumed by the death of countless Jedi who were fired upon by their own soldiers. At Sidious's direction, Vader then left for the planet Mustafar to wipe out the Executive Separatist Council and bring an end to the Clone Wars once and for all, leaving behind the 501st to keep the Temple locked down. To root out any surviving Jedi, the Temple's recall beacon was also activated to spread a false message of hope, requesting all Jedi to return to Coruscant as a way to lure any survivors back to the occupied building. To further entrap survivors, some clones wore Jedi robes to make themselves look like Jedi and ambush any real Jedi who approached.

Amongst the survivors was Kenobi, who escaped from the 212th Attack Battalion and met up with Grand Master Yoda and a Jedi sympathizer, Senator Bail Prestor Organa, on the Tantive III. Upon learning of recall message, Kenobi rallied his allies to return to Coruscant and shut down the beacon, with Yoda agreeing and noting it would allow them to learn more about their enemies. As Kenobi and Yoda entered Coruscant's orbit aboard the Tantive III, the starship received a message from Vice Chair Mas Amedda, who ordered Organa to attend a special session of Congress that Palpatine would be having. While Organa initially assumed it could be a trap, Kenobi realized that Palpatine would need the Galactic Senate intact to control the galaxy, and Yoda explained the sudden session only aided in their mission, as it turned attention away from the Temple. During that special session, Palpatine claimed to the Senate that the Jedi had tried to overthrow the Republic and transformed the Republic into the Galactic Empire, which was meet with cheers by most of the Senate. With the public desperate for peace after the Clone Wars, the Empire was accepted by many across the galaxy.

Arriving outside the still-smoking Jedi Temple, Kenobi, who was saddened by the sight of the smoke, and Yoda fought their way into the building through the 501st. Kenobi was also distressed by the sight of the clones wearing Jedi robes as a trap. Once inside, they were met with the aftermath of the attack Vader and the 501st had carried out, which horrified Kenobi more than the smoke and clones had. Recognizing lightsaber burns on the body of a Padawan but unaware of Skywalker's fall into darkness, the two were left to ponder who had lead the attack, although Kenobi did ponder if a Sith Lord was responsible. Thanks to their knowledge of the Temple's layout, Kenobi and Yoda were able to easily avoid the clones inside the building. With Yoda keeping watch, Kenobi made his way to reprogram the Jedi beacon. Yoda also learned of Skywalker's fall from the security recordings. Kenobi's work was inspired by a question once asked of him by the youngling Caleb Dume, who had asked whether the beacon could be configured to order Jedi away from the Temple instead of to it.

Kenobi's new message warned of the rising Empire and requested survivors to stay away from the Temple, promising them that a new hope would emerge despite the darkness facing the galaxy. Having since become the Padawan to Jedi Master Depa Billaba, who fell during Order 66 to give him time to escape, Dume himself was lured to Coruscant by the fake message. Eager to return to the Temple on the belief that the Jedi Masters had created a plan, he stole the smuggler Janus Kasmir's ship the Kasmiri, which was quickly reported stolen to the Empire, from the planet Kaller and traveled through hyperspace to reach the Coruscant system. At the exact same time as when Kenobi sent the new message, Dume was about to come out of hyperspace. Suddenly receiving Kenobi's message just before he was surrounded by Aggressive ReConnaissance-170 starfighters, Dume escaped the ensuing ambush back to Kaller.

Kept in the hands of other surviving Jedi, Kenobi's message of hope survived for years to come. After sending out his new message, which both assumed the clones would not find for some time, Kenobi ignored Yoda's objections to check the security records, leaving him horrified upon learning of his friend's fall to the dark side. Although he demanded to be sent after Sidious on the belief that he would be unable to confront Skywalker, with whom Kenobi shared a brother-like bond, Kenobi ultimately agreed to go after his former friend when Yoda noted he was not powerful enough to battle the Sith Master. With their respective missions clear, both Jedi left the Temple, with Yoda leaving to confront Sidious in the Galactic Senate Building while Kenobi, after Yoda noted he knew what lead to follow to find the newly-christened Vader, met with Amidala at her apartment.

Kenobi and Yoda's attempts to dethrone the Sith just as their reign began ended in failure. Yoda was defeated by Sidious and fled into exile, while Kenobi, sneaking aboard Amidala's J-type Naboo star skiff after she refused to give him her husband's location, arrived on Mustafar and dueled Vader, who lashed out in anger at Amidala on the fear she had brought Kenobi to the planet to kill him. Although he assumed his former friend died after leaving him to burn by the planet's lava flows, Vader survived and was reconstructed, relying on a suit of life-support armor due to his injuries. Shortly afterward, Vader and Sidious stood in the shadows of the Jedi Temple to watch a celebration of the Jedi Order's eradication on the building's steps. The Temple was then turned into the Emperor's personal palace.

• Skywalker: A Family at War