Mission to Mustafar 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 the lava planet of 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 Mustafar under the guise of protecting them . 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 told 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 . Prelude . Nineteen years before the Battle of Yavin , of 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 prison er 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 General s 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 . 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 facility on Mustafar . The Separatist Council ' s decision to go to Mustafar was also 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 . 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 . The newly - anointed Sith Lord attacked the Jedi Temple and the chancellor issued a command for the clone trooper s 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 was ordered to go to the Mustafar system and destroy the Separatist Council . The mission . With the destruction of the Jedi Order underway across the galaxy , Vader pilot ed his Jedi starfighter , 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 Separatist Council members via hologram , with Gunray remarking confidently that the plan of the Council had gone just as Sidious had promised . Though Gunray and the others did not know what was about to happen , the Dark Lord promised that his new apprentice would soon arrive to take care of them and the leadership proceeded to continue monitoring the aftermath of the Clone Wars unaware of their fate . Once Vader landed , leaving Artoo with the starfighter , he entered the mining facility and was greeted by Gunray and the other Separatists . The Sith Lord used the Force to seal the doors in the room where they were standing , ensuring that none of the Separatists could escape . Vader began his slaughter of the Separatists once the room was secured , taking them out one by one with his lightsaber ; he also destroyed the B1 Security Battle Droid s , an OOM command battle droid , and Neimoidian guards and aides who had assembled in the room with their leaders . In rapid succession , Vader executed the Separatists including Po Nudo , Senator of the planet Ando , 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 Seperatists after defecting to the Republic Special Weapons Group . After Vader killed Poggle , he then killed Wat Tambor , Foreman of the Techno Union , who fled into a conference room , and Settlement Officer Rune Haako of the Trade Federation were also soon killed . By the end of the slaughter , only Gunray remained . The viceroy begged for mercy and said that Sidious promised them peace , but Vader cut him down as well , bringing an end to the Separatist Council . As Vader ' s slaughter began , the chancellor — scarred and deformed from Force lightning during his duel with the Jedi Council — went 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 , the chancellor 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 thunderous applause from the Senate . Several hours after Vader spoke with Sidious from Mustafar via hologram and informed his master that the Separatist Council had been eliminated . The Emperor praised his apprentice for restoring peace and justice to the galaxy , and he ordered Vader to send a message to the Trade Federation Droid Control Ships that would shut down the battle droid s of the Separatist Droid Army . In doing so , the Clone Wars officially came to an end . The new Empire was victorious . Aftermath . After speaking with Sidious , 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 . By the end of the fight , Vader was left horrifically burned from a lava river . Kenobi fled with Artoo and Amidala , who secretly gave birth to twin s 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 . The remaining government and military elements of the Separatist Alliance , left leaderless without the Separatist Council , retreated from prominence and broke into various holdouts that continued to exist for a number of years . Most of its star system s , however , eventually surrendered to the Imperial regime and became part of the New Order . 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 moon s support of the Separatist Alliance during the war . Following the execution of the Separatist Council , Arsin Crassus channeled the former Confederacy ' s financial resources into the the coffers of the newly expanding Galactic Empire . Crassus became an important Imperial financier during the Imperial Era . Despite the efforts to eliminate secessionist thought , a group of rebels formed the Alliance to Restore the Republic and fought against the Empire during the Galactic Civil War , ultimately leading to the fall of the Galactic Empire . Sometime prior to 0 BBY Darth Vader would construct a castle on Mustafar . Behind the scenes . Darth Vader ' s mission to Mustafar and his assassination of the Separatist Council were depicted in the 2005 film , written and directed by " Star Wars " creator George Lucas . The mission of Mustafar was later explored in Canon literature such as Chuck Wendig ' s 2015 novel " Aftermath " and James Luceno ' s 2016 tie - in novel " " .