In the third year of the Clone Wars, Darth Sidious—the Dark Lord of the Sith who was publicly known as Supreme Chancellor Palpatine of the Galactic Republic—sent his apprentice, Darth Vader, on a mission to Mustafar to kill the Separatist Council, the wealthy and influential backers of the late Count Dooku and the Confederacy of Independent Systems. Sidious, who secretly controlled the Separatist Alliance as part of his plot to take over the galaxy, had sent the Separatist Council to the volcanic planet Mustafar under the guise of protecting them, where their power collapsed after the Battle of Utapau. When Vader arrived, however, he assassinated each member of the Separatist Council in order to bring an end to the Separatist rebellion against the Republic. As Vader arrived on Mustafar, Chancellor Palpatine publicly declared himself as the galaxy's Emperor and transformed the Republic into the Galactic Empire.
Vader contacted his master after the Separatist Council members were killed, and the Dark Lord ordered him to shut down the Separatist Droid Army. In doing so, the Clone Wars came to an end. Senator Padmé Amidala, Vader's wife, soon arrived on Mustafar in an attempt to bring Vader, who had been the Jedi Knight Anakin Skywalker, back to the light. She failed, and Vader engaged in a lightsaber duel with Jedi Master Obi-Wan Kenobi, a fight that left Vader brutally scarred and in need of a life-supporting suit of armor for the rest of his life. In the years that followed, some holdouts of the Confederacy continued to operate throughout the galaxy despite the end of the war. The Imperial Military tracked these holdouts down to destroy them and absorb their technology into the Imperial regime.
Nineteen years before the Battle of Yavin, during the Clone Wars that were fought between the Galactic Republic and the Confederacy of Independent Systems, Supreme Chancellor Palpatine—secretly Darth Sidious, the Dark Lord of the Sith, who controlled both factions—orchestrated his own kidnapping from Coruscant, the capital planet of the Republic. The chancellor was made to appear to be the prisoner of the Separatist Head of State, Count Dooku, a fallen Jedi and the Sith apprentice of Darth Sidious. The Grand Army of the Republic, led by Jedi Generals Obi-Wan Kenobi and Anakin Skywalker, fought to rescue the chancellor during the Battle of Coruscant. The two Jedi found the chancellor on the Invisible Hand, the command ship of the cyborg General Grievous, where they engaged Count Dooku in a lightsaber duel. Skywalker got the upper-hand during the fight, and, at the chancellor's goading, the Jedi Knight executed Dooku. The count's loss was a major setback for the Separatist Alliance. However, Grievous and the Separatists were unaware that Sidious betrayed and orchestrated the death of Dooku.
Nute Gunray and the other Separatist leaders as the Clone Wars draw to a close.
The Separatist Council, comprised of wealthy and powerful corporate titans who backed Dooku and his Separatist rebellion against the Republic, gathered on the planet Utapau and awaited guidance from General Grievous in the aftermath of Dooku's death. Grievous, on the orders of Darth Sidious, told the Separatist Council that he was sending them to the lava planet of Mustafar in the Outer Rim Territories for their safety. Nute Gunray, the Viceroy of the Trade Federation and a member of the Separatist Council, expressed doubts that the cyborg general could keep them safe after Chancellor Palpatine escaped from his ship, but the council nonetheless followed the general's directive and gathered in a mining complex on Mustafar, where a secret command center was built onto the mining complex to serve the council, while the decision to go to Mustafar was influenced by Arsin Crassus, a Trade Federation employee.
As the war's final days progressed, Grievous was killed by General Kenobi during the Battle of Utapau. The defeat of Grievous resulted in the collapse of any functional command structure for the Separatist military, effectively ending the war despite the many battles still being waged across the galaxy. Meanwhile, the chancellor manipulated Skywalker towards the dark side of the Force. Skywalker, who had been having visions of his pregnant wife, Senator Padmé Amidala, dying in childbirth, was led to believe that the chancellor had the power to save people from death. Soon thereafter, Skywalker discovered the chancellor's Sith identity and informed Jedi Master Mace Windu. Along with three other members of the Jedi High Council, Windu attempted to arrest the chancellor, leading to a lightsaber duel that left the four Jedi Masters dead.
Skywalker, who helped the chancellor defeat Master Windu, pledged himself to Darth Sidious and was given the Sith name of Darth Vader. Sidious ordered the newly-anointed Sith Lord to attack the Jedi Temple, and then destroy the Separatist Council on the Mustafar system. While Vader is at the Jedi Temple, temple, Sidious issued a command for the clone troopers of the Grand Army of the Republic to kill their Jedi leaders, in retaliation for what the chancellor publicly stated was the Jedi Council's foiled attempt to assassinate him and take over the Republic. After the attack on the Jedi Temple, Vader headed to the Mustafar system.
The Separatist Council on Mustafar shortly before their death
With Grievous' death at the hands of Kenobi on Utapau, Gunray now found himself as the acting Head of State of the remaining Separatist forces, and he, along with the other members of the council, continued to observe Separatist combat operations across the galaxy from the complex's command center.
With the destruction of the Jedi Order underway across the galaxy, Vader piloted his Jedi interceptor, accompanied by his astromech droid R2-D2, to Mustafar to carry out his assassination orders. As he approached the mining facility, Sidious spoke to the Viceroy Nute Gunray and the rest of the Separatist leadership, which had continued to destabalize in the aftermath of Grievous' death, the Dark Lord remarked confidently that the plan of the council had gone just as Sidious had planned. Though the Viceroy and the others did not know that they were being betrayed by Sidious, the Sith Master promised that his new apprentice would soon arrive to "take care of them," under the pretext of peace talks at resolving the conflict. The leadership thus was reassured and proceeded to continue monitoring the last moments of the war, unaware of their pending fate. Vader soon landed, leaving Artoo with the starfighter.
Vader kills Poggle the Lesser.
As Lord Vader arrived on Mustafar, the chancellor—deformed from Force lightning during his duel with the Jedi Council—appeared before the Galactic Senate and claimed that the Jedi had attempted to rebel against him and take over the Republic. Promising to restore peace, security, and stability after three years of war, Palpatine proclaimed that the Republic was to be reorganized into the First Galactic Empire, with himself as the galaxy's emperor. The move was met with a roaring applause from the rechristened Imperial Senate. However, Padme Amidala expressed her dissatisfaction at this speech.
Once the Emperor's enforcer entered the mining facility, he was greeted by Gunray and the other Confederate leaders whom sought peace with the Galactic Empire. However, the Sith Lord silently used the Force to seal the doors in the room where they were standing, ensuring that none of the Separatists could escape. Vader then began his slaughter of the Separatists once the room was secured, taking them out one by one with his lightsaber; he also destroyed the OOM-series security droids, an OOM command battle droid, and Neimoidian guards and aides who had assembled in the room with their commanders. In rapid succession, Vader executed the Separatists including Po Nudo, Senator of the planet Ando.
Vader in the Separatist Council war room.
Vader then killed the Neimoidian Rute Gunnay, Magistrate Passel Argente of the Corporate Alliance, and Shu Mai, Presidente of the Commerce Guild. He then set his sights on San Hill, Chairman of the InterGalactic Banking Clan, Senator Tikkes of Mon Cala and Archduke Poggle the Lesser, who had recently returned to the Separatists after defecting to the Republic Special Weapons Group. After Vader had killed Poggle, he killed Wat Tambor, Foreman of the Techno Union, who fled into a conference room, and Settlement Officer Rune Haako of the Trade Federation. By the end of the massacre, only Gunray remained and attempted to flee, however Vader then jumped in front of him. The viceroy pleaded for mercy and said that Sidious promised them peace, but Vader interrupted him by cutting him down, bringing an end to the Separatist Council.
Darth Vader brutally ended the three-year long Clone Wars.
The fallen Jedi then spoke with the new emperor of the galaxy via hologram and informed his master that the Separatist leaders had been eliminated. With them out of the way, he ordered his new apprentice to transmit the order to all the Trade Federation Droid Control Ships to deactivate all remaining battle droids of the Separatist Droid Army immediately.
This final act allowed the last of the fighting to end throughout the galaxy, including on Lokori. In doing so, the Clone Wars officially came to an end as suddenly as it had started three years prior. Thus, the new Empire had achieved a swift victory and ensuring the New Order stood unopposed.
Vader, enraged, strangled his wife.
After speaking with Sidious and fulfilling his wishes, Vader saw Amidala's ship arrive on Mustafar; she secretly followed him there after Kenobi told her that Skywalker turned to the dark side. She pleaded with him to run away with her and leave their troubles behind, but Vader refused—he said he turned to protect her, and that his new power would "keep her safe" and that he could overthrow the Emperor and they rule the Empire together. Though she tried to make him see reason, Vader noticed that Kenobi was standing in her ship. He too followed Vader to Mustafar, sneaking aboard Amidala's ship without her knowledge. An enraged Vader attacked his pregnant wife and knocked her unconscious, leading to a brutal lightsaber duel between Vader and his former Jedi Master. Vader was horrifically mutilated in the duel and was left by Kenobi for dead, burning on the bank of a lava river. Kenobi fled with Artoo and Amidala, who secretly gave birth to twins before dying as Vader had foreseen, while the Emperor arrived on Mustafar to tend to his wounded apprentice. Vader was forced to wear a cybernetic suit of armor for the rest of his life in order to survive.
In the wake of the execution of Viceroy Gunray—whose execution was covered up in official records, which instead claimed he took his own life after the Separatist Council realized victory was unlikely—Arsin Crassus channeled the late Separatist leadership financial resources into the coffers of the newly expanding Galactic Empire. Crassus became an important Imperial financier during the Imperial Era. Without its leadership, the Confederacy of Independent Systems collapsed and broke into various holdouts, which mostly retreated to the Western Reaches that continued to exist for a number of years, some not even realizing the war was over, and carried on fighting the Empire.
Most of its star systems, however, eventually surrendered to the Imperial regime and became part of the New Order after a number of pacification operations. The Imperial Military saw to the dismantling of the Separatist fleets across the galaxy, such as the Bilbringi shipyards, and appropriated its various droid models and technology to suit the Empire's purposes. Massive crackdowns also occurred on Confederate sentiment in order to wipe out the secessionist tendencies that had troubled the Republic. One such event was the Antar Atrocity, in which Moff Wilhuff Tarkin led Imperial forces in mass arrests, executions, and massacres on Antar 4 as punishment for the moons support of the Separatist Alliance during the war.
Concept art for Vader's attack, by Ryan Church.
The mission to Mustafar first appeared in the 2005 film Star Wars: Episode III Revenge of the Sith, the third and final installment of the Star Wars prequel trilogy.
In the DVD commentary of Revenge of the Sith, George Lucas stated that the interwoven scenes of the Mission to Mustafar and the Proclamation of the New Order was an homage to the christening and assassination sequence of the 1972 classic film The Godfather, directed by his friend Francis Ford Coppola.
A scene present in Episode III's screenplay, which didn't make it into the film, had Nute Gunray and Rune Haako hiding under a table as Darth Vader kills the Separatist Council, as seen in Ryan Church's concept art. Panicked, Haako attempted to flee only to die at Vader's hands as seen in the film, leading Gunray to get out from under the table and activate the control panel for the doors to open. As the remaining Separatists were killed, droidekas entered and opened fire on Vader. Gunray watched as the smoke cleared and found Vader gone. Vader then drops down from the roof and destroys the droids, after which he jumps over to Gunray and beheads him. This explains why Gunray is so surprised when Vader jumps at him—he thought he had been killed by the droids.
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