Yoda and two stealth troopers walk out onto a sinkhole with their transport in the distance. Yoda looks out over the sinkhole and sees very little. "Our intel tells us that the Trade Federation will rendezvous here," one of the stealth troopers explains, "The Chancellor's orders are that we wait here and arrest them on site." Yoda looks at them suspiciously, "For now... I shall wait." Then he winces, closes his eyes, and holds his head. He feels a disturbance in the Force.
"Is everything alright, General Yoda?," the second trooper asks.
Yoda looks at them carefully, but says nothing.
Elsewhere on Utapau, the Jedi lead Clone Troopers on an assault of the compound. They race across a bridge as a droid army advances. The Clone Troopers take position and fire, blasting several droids as the Jedi, led by Ki-Adi-Mundi, cross over and begin slashing the droids to pieces. Inside the compound, a commander droid faces a hologram of Viceroy Gunray who exclaims, "Stand your ground! No not let the Republic forces -," the hologram fades. A droid sitting at the communication console turns and tells his commander, "Communication channels have been jammed, sir." Several Jedi drop from the ceiling and begin hacking away at the droids. Shaak-Ti and her padawan engage the two guard droids and deflect their electrical staffs before cutting them in half. The Jedi Plo Koon flues his Jedi fighter, leading a group of clone fighters to attack the transport ships attempting to escape. They launch a volley of attacks, damaging the ships before Clone dropships finish them off with missiles, blasting them from the sky. In a city area, Obi-Wan drives his lizard through the street toward a droid blockade. Before they get the chance to fire on him, he has his lizard stomp them into the ground.
Back on Curuscant, Palpatine is putting on his dark cloak: he is now fully Darth Sidious. He turns to Anakin, "Because the Council did not trust you, my young apprentice, I believe you are the only Jedi with no knowledge of this plot. When the Jedi learn what has transpired here, they will kill us, along with all the Senators."
"The Jedi's next move will be against the Senate?," Anakin asks in a confused tone, "But Padme and Senator Organa have always been allies of the Jedi."
"Every single Jedi, including your friend Obi-Wan Kenobi, is now an enemy of the Republic. You understand that, don't you?"
"I... understand, Master."
"We must move quickly. The Jedi are relentless; if they are not all destroyed, it will be civil war without end. First, I want you to go to the Jedi Temple. We will catch them off balance. Do what must be done. Only then will you be strong enough with the darkside to save Padme."
"Yes,... my Master," he turns in a daze and leaves.
With Anakin gone, Sidious turns and produces a hologram disc. "Attention all commanders, the time has come. Execute Order 66," he commands. On the bridge in Utapau, a commander receives the message on his disc. A smaller hologram of Sidious commands him, "Execute Order 66." The commander nods and turns to his men, "Execute Order 66." His men nod back, Yes, sir." The troopers rush out onto the bridge and begin firing. Several Jedi are shot in the back. A few turn and deflect bolts back at the troopers before being shot. Ki-Adi-Mundi decapitates the final droid, then looks up as if sensing something. He turns and deflects several bolts back at the troopers, taking out a few before running to the other side of the bridge as more blaster bolts are launched his way.
The Jedi Aayla Secura and a few other Jedi march through a nearby forest along with a group of troopers and a few walking-tanks. A commander in a tank receives Sidious' hologram message, "The time has come. Execute Order 66." Aayla turns as if sensing something just as the troopers fire on her and the others. She falls under some foliage and the troopers continue to fire.
Yoda drops his cane, clutches his chest, and rests along the rim of the sinkhole. One of the stealth troopers opens his holographic disc and gets a message from Sidious, "Execute Order 66." The two troopers say nothing, but march up behind Yoda with their blasters ready. Yoda looks up as if sensing something, ignites his lightsaber, and backflips toward the two troopers. A second later, the troopers fall dead along with their damaged helmets rolling along the ground.
Near a river close to a cliff, a commander gets Sidious' message, "Execute Order 66." Just then, Obi-Wan races his lizard toward the edge of the cliff. "I am General Obi-Wan Kenobi," he calls down, "I demand to know why there are trooper sin this area." They say nothing. Instead, a trooper kneels down with a rocket launcher and fires. The missile hits just below the lizard, but the impact drops both of them down the cliff. Obi-Wan splashes down into the water.
At the same time, Anakin and a platoon of Shock Troopers armed with flame throwers march to the Jedi Temple. Anakin walks through the Jedi Temple, first entering the library. "Burn everything," he commands and the troopers begin torching the rows of information logs. Thousnads of years of information begin instantly going up in flames. As one trooper rounds the corner, a lightsaber slashes across his armored chest. Jocasta Nu reveals herself, a lightsaber in hand, "What are you doing in my library?" The clones part ways and Anakin emerges. She is taken aback, "Anakin Skywalker?". He ignites his red saber, "I am sorry," and then launches forward with an attack.
Upstairs, a group of Younglings huddle together. One of them speaks up, "There are too many of them. What are we going to do?" The door slides open and they turn in time to see a group of Troopers entering the room. On the top level, a group of Troopers enter the Jedi Council room and begin torching the seats. Another trooper enters the garden and the plants soon catch fire, On another level, a Trooper enters a meditation room and sets it on fire. Anakin is on a different level engaging with two Padawans and the Jedi knight Cin Drallig. He slashes one padawan across the chest, while kicking Drallig in the chest to create some distance. The third padawan launches himself at Anakin, but he moves back while slashing across the midsection. Drallig picks himself up, nut Anakin uses the Force to choke him, bringing him back to his knees. Once there, Anakin marches forward with a slash.
Outside, the Jedi Temple is on fire. Large plumes of smoke billow toward the sky as Anakin walks out of the building, followed by his Troopers. Once he makes it to a nearby transport, a commander shows him a holographic disc, "A message for you, my lord." Sidious appears and tells him, "There are more Jedi on Utapau. Hunt them down and eliminate them... all of them."