Operation Knightfall

Operation Knightfall had occured after the First Duel on Coruscant had failed and Anakin Skywalker became Palpatine's second and final apprentice, Darth Vader.

Attack
Darth Vader had been ordered to attack the Jedi Temple. He arrived with members of the 501st Legion and killed many Temple Security Forces. While the clones dealt with the temple guards, Anakin ran into the Jedi Archives and killed many Jedi, including Jocasta Nu. He then proceeded into the halls to find clones being killed by Jedi. He gained the upper hand by using remains of a temple statue to crush several Jedi. Mace Windu and Kit Fisto, who had been interrogating their three year prisoner Jango Fett in revealing the location of the Trade Federation remnants, learned of the attack and freed Jango Fett. They told him to kill whoever was killing Jedi and if he saved the Jedi, he would be freed. Jango accepted and once more put on his bounty hunter armor and led an assault to kill many clones. Mace Windu and Kit Fisto waited in the prison chambers until further notice. Vader had taken control of the hangars, and then the recording rooms. He sent a message to lure all Jedi back to Coruscant, where he would kill them. A clone commander informed Vader that master Cin Drallig and his padawans had penetrated their upper level defenses. Vader left the clones in charge of the beacon. Vader quickly stopped by the council chambers and killed all of the Jedi younglings present. He then went to the meeting rooms and discovered Drallig's padawans defeating the last of the clones. Vader then engaged into a duel against all and killed Serra Keto just as Cin Drallig arrived. Vader and Drallig dueled, which resulted in the death of the famous swordsman. Anakin then received a message that the prison levels were being defended by the Jedi and that many Jedi are fleeing. Vader walked down the corridors and engaged Kit Fisto into a duel. The two fought, but the duel led to the death of Fisto at the hands of Vader. Meanwhile, Jango Fett and his Jedi battalion had been slayed by the clones. Vader then engaged Mace Windu, who was one of the last Jedi at the temple. The duel led to Mace being stabbed by his former friend. Vader then read the recordings and learned that the Trade Federation had been hiding on Mustafar. He informed Darth Sidious that the Trade Federation was hiding on Mustafar. His second mission was to head to Mustafar and slaughter the remnants of the Trade Federation.

Order 66
While Darth Vader slaughtered many Jedi in the temple, Palpatine called every clone trooper to execute Order 66. Many Jedi had been killed, but most of the Jedi Council had survived. Obi-Wan had escaped off of Utapau, Yoda saved Chewbacca and Tarfull on Kashyyyk, Ki-Adi-Mundi fleed Mygeeto, Plo Koon left Nar Shaddaa, Adi Gallia dissappeared off of Saleucami, but many Jedi Knights and young padawans were killed including Aayla Secura and Barriss Offee on Felucia, Luminara Unduli slaughtered on Ilum, Quinlan Vos on Boz Pity, most Jedi fled the Jedi Temple during its attack, such as Shaak Ti, Kazdan Paratus, Even Piell, Coleman Kcaj, and a few younglings. Rahm Kota, who did not trust clones and used his own militia, saved his own life and fled into the Outer Rim along with his militia.

Visiting the Ruins
Senator Bail Organa and Raymus Antilles used a homing beacon from the now-dead Saesee Tiin's ship, The Sharp Spiral, to find several Jedi. Obi-Wan, Yoda, and many others broke into the Jedi Temple and discovered a holographic recording of Anakin slaying Mace Windu and bowing down before Palpatine. Many Jedi went into hiding while Obi-Wan went to find Anakin and Yoda went to find the Emperor.