Mission to Mustafar

"The traitors have been taken care of, Lord Sidious.''" "''Good... Good... you have done well, my apprentice. Now Lord Vader, go and bring peace to the Empire."

- Darth Vader and Darth Sidious

At the end of the Clone Wars, the Sith Lord Darth Sidious sent his new apprentice, Darth Vader, on a mission to kill the reminding high ranking leaders of the Confederacy of Independent Systems who had gathered on the volcanic world of Mustafar to tie up the loose ends in Sidious' plot to cement his total rule over the Galactic Republic after Order 66 had been carried out across the galaxy. Vader dutifully carried out the massacre after he trapped the Separatist Council in their command center, where he executed them one by one. The massacre came to an end with the death of Nute Gunray, the Viceroy of the Trade Federation and one of the most influential Separatist leaders.

As the slaughter was taking place, Sidious&mdash;known in public as Supreme Chancellor Palpatine&mdash;addressed the Galactic Senate and proclaimed that, in the interest of galactic security, the Republic would be transformed into the Galactic Empire. After the bloodshed and the rise of the New Order, the new Emperor ordered his apprentice to shut down the Separatist battle droids, thus finally ending the Clone Wars. Afterward, before Vader could leave Mustafar, he was confronted by his wife, Senator Padmé Amidala, who attempted to turn him away from the dark side of the Force. The arrival of Jedi Master Obi-Wan Kenobi led to a lightsaber duel between Vader and his former master, one in which Vader was left brutally disfigured and left living in a suit of armor for the rest of his life.

Prelude
"The Chancellor has given me a very important mission. The Separatists have gathered in the Mustafar system. I'm going there to end this war. Wait for me until I return&hellip; things will be different, I promise."

- Darth Vader to Padmé Amidala



During the battle over Coruscant, Count Dooku was executed by the Jedi Knight Anakin Skywalker. Following this loss, General Grievous of the Separatist Droid Army, became the leader of the Separatists as well and took control of the Separatist Council, which at the time was based on the planet Utapau. Grievous under Sidious's guidance was to transfer the Council from Utapau to Mustafar as Sidious knew of the impending offensive, that would eventually lead to Grievous' own demise at the hands of Jedi Master Obi-Wan Kenobi. Shortly after this Viceroy Nute Gunray of the Trade Federation who was one of the Confederacy corporate backers; become it Head of State as the three years of fighting drew to a close across the galaxy.

Following the destruction of the Jedi Order, Sidious ordered his apprentice to go to Mustafar and kill the surviving members of the Separatist Council. Sidious told Nute Gunray, the Viceroy of the Trade Federation, who was in the war room within the bunker; that his apprentice would reward them for their loyalty during the Clone Wars by 'taking care' of them as they viewed the holotables that displayed live feeds from various battlefronts keeping them up-to-date on events in the galaxy while they were safely locked away.

The mission
"The plan has gone as you had promised, my Lord.''" "''You have done well, Viceroy. When my new apprentice, Darth Vader, arrives, he will take care of you."

- Head of State and Viceroy Nute Gunray and Darth Sidious

The assassinations
"The war is over. Lord Sidious promised us peace! We only want—"

- Nute Gunray's last words



Darth Vader traveled swiftly to Mustafar system with R2-D2 as the Galactic Republic was reformed into the First Galactic Empire by Darth Sidious. Upon arrival, Vader ordered R2 to told to stay with the ship on the landing platform as he proceed onwards to the bunker. After he arrived at the war room, Nute Gunray who was Head of State as well as San Hill and the other members of the council welcomed and greeted him.

Vader however instead silently closed the doors of the bunker, trapping the leaders inside and began a rampant killing spree, even destroying the battle droids and killing the Neimoidian guard's as he swiftly and without mercy single handedly eliminated the entire Confederacy leadership using his new found Sith powers and those he had learned as a Jedi. Vader first slaughtered Denaria Kee, Aito Laff, Po Nudo, and Passel Argente. The remaining Separatists fled. Vader went after them and killed Nudo's Shi'ido aide, Cat Miin and Shu Mai. Vader then strode after and killed Tikkes, San Hill, Nudo's Aqualish aide, Poggle the Lesser and Rute Gunnay next while Nute Gunray watched in horror. Rune Haako and Wat Tambor fled into the conference room to avoid Vader, but Vader slaughtered both Haako and Tambor. Vader finally cornered Nute Gunray, whom he despised most of all for his attempts to kill Padmé Amidala, Vader's wife. Gunray pleaded for his life but to no avail; Vader executed him. As he surveyed the carnage, his eyes turned a red-rimmed yellow, a trait common among those immersed in the dark side.

Sending the shutdown signal
"Send a message to the ships of the Trade Federation, all droid units must be shut down immediately!"

- Emperor Palpatine to Darth Vader

With the death of the Separatist Council and the Galactic Republic transform into the Galactic Empire in the Imperial Senate, Vader soon received the order from Emperor Palpatine via hologram from Imperial Center to send a shutdown signal to the Trade Federation droid control ships that all droid units were to deactivate immediately across Confederacy space; to prevent the Confederacy of Independent Systems from posing any threat to the New Order.

Aftermath
"The Separatists have been taken care of, my master.''" "''It is finished, then. You have restored peace and justice to the galaxy."

- Darth Vader and Darth Sidious

After the completion of his mission, Vader set his gaze over the surface of Mustafar before he was confronted over his actions by his wife, Senator Padmé Amidala, who could not believe what he had become and done, and tried to turn him back to the light. Unfortunately for Amidala, his former master Obi-Wan Kenobi, had stowed aboard her vessel, and when Vader realized this, he force choked her and then initiated a lightsaber duel with Kenobi, who also attempted to turn Vader away from the darkness, but the young Sith Lord was too furious to be reasoned with, leading Kenobi to grievously wound Vader, who, after his immolation, was left on a river of lava to die. The Emperor, would after sensing his apprentice in trouble; departed and arrived on the planet along with a dozen clone stormtroopers, and took his apprentice's ruined body to Imperial Center, where Darth Vader was rebuilt into the figure who was feared, as the Empire's most deadly servant.

Shortly after the Clone Wars ended, the Confederacy of Independent Systems and the remaining secessionist systems that made it up; were now leaderless and without it's droid army, eventually surrendered to the new regime that had replaced the Republic, while some remnants managed to retreat; forming into various holdouts that continued to be active until at least four years before the Battle of Yavin as the Empire began to oversee the dismantling of their fleets right across the galaxy such as at the Bilbringi shipyards and sought the appropriation of various droid models and technology over a period of four years. Massive crackdowns also occurred on Confederate sentiment was also conducted on several worlds in an effort to wipe out all secessionist tendencies that had troubled the Old Republic.

Appearances

 * Star Wars: Episode III Revenge of the Sith