Mission to Mustafar

"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

At the end of the Clone Wars, Darth Sidious, having declared himself Emperor of a new Galactic Empire, transformed from the remains of the Galactic Republic, sent his new apprentice, Darth Vader on a mission to eliminate the leadership of the Separatist Council on Mustafar, thus ending the war.

Prelude
"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."

- Viceroy Nute Gunray and Darth Sidious



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 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, with no immediate civilian or military official to take the head of state post, it instead transferred to the Viceroy Nute Gunray of the Trade Federation who was one of the Confederacy corporate backers; effectively exposing it as a corporatocracy as the 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, that his apprentice would reward them for their loyalty during the Clone Wars by 'taking care' of them.

The mission
"Welcome, Lord Vader. We've been expecting you."

- Head of State Nute Gunray

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 control center at the heart of the bunker, Nute Gunray who was Head of State as well as San Hill and the other members of the council greeted him and wished to sue for peace with the Empire and wished for an end of the Clone Wars.

Vader instead silently closed the doors of the bunker, trapping the leaders inside and began a rampant killing spree, even destroying the battle droids before looking for his targets. By using his new found Sith powers and those he had learned as a Jedi, he swiftly and without mercy single handedly eliminated the entire Confederacy leadership. As the killing began, the remaining Separatists attempted to escape but Vader went after them and killed the rest of them while Gunray watched in horror as some fled into the conference room only to be slaughtered before he finally cornered Gunray who pleaded for his life, but to no avail as Vader executed him.

Sending the shutdown signal
With the death of the Separatist Council and the re-organization of the Galactic Republic into the Galactic Empire during the Proclamation of the New Order in the Imperial Senate, Vadar received the order from Emperor Palpatine via hologram from Imperial Center to send a shutdown signal to all Trade Federation droid control ships that the entire Separatist Droid Army deactivate immediately to prevent the Confederacy of Independent Systems from posing any further threat to the Empire.

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, Padmé Amidala, who could not believe what he had become and done. Unfortunately for Amidala, Vader's former master Obi-Wan Kenobi, had stowed aboard her vessel, and when Vader realized this, he force choked her and then initiated a duel with Kenobi, one that would ultimately leave him badly maimed for the rest of his life.

Shortly afterwards, without their droid army and navy to protect them, the remaining Separatist systems were forced to surrender and were occupied by the Empire following the conclusion of the Clone Wars who would over a period of four years, be overseeing the dismantling of their fleets right across the galaxy such as at the Bilbringi shipyards and began the appropriation of various droid models and technology. Massive crackdowns on Confederate sentiment was also conducted on several worlds in an effort to wipe out all secessionist tendencies while some remaining Separatists managed to retreat into various holdouts.

Appearances

 * Star Wars: Episode III Revenge of the Sith
 * Star Wars: Darth Vader 6: Vader, Part VI