Mission to Mustafar / Legends In 19 BBY , Darth Sidious , the Dark Lord of the Sith and Supreme Chancellor of the Galactic Republic , sent his new apprentice , Darth Vader on a mission to kill the remaining members of the Separatist Council on the volcanic planet of Mustafar . The Council , consisting of the surviving top members of the Confederacy of Independent Systems , was a loose end in Sidious ' plot to gain control of the Republic and mold it into the galaxy ' s first empire . Vader willfully carried out the slaughter after he trapped the council in their war room , where he slew each Separatist leader , one by one . The slaughter ended with the death of Nute Gunray , the Viceroy of the Trade Federation , who was one of the most influential members of the Council . As the bloodshed came to an end , Vader received the order to send a shutdown signal to all battle droids part of the Separatist Droid Army , ending the Clone Wars , that , for the past three years , had spread across the galaxy . This , coupled with the Chancellor ' s Declaration of a New Order before the Galactic Senate , secured Sidious ' position as the Galactic Emperor of the New Order . Before Vader could leave the planet , he was confronted by his wife , Senator Padmé Amidala of Naboo , who inadvertently smuggled Vader ' s old master , Obi - Wan Kenobi , to Mustafar . Confusion ensued when the Jedi Master revealed himself , and Vader , believing that Amidala had brought Kenobi to kill him , flew into a rage , and Force choked Amidala ; she survived her husband ' s wrath , but was knocked unconscious . Kenobi attempted to turn Vader away from the darkness , but the young Sith Lord was too furious to be reasoned with , and he attacked his former teacher , beginning an epic duel between the two former brothers - in - arms , in which Kenobi grievously wounded Vader , who , after his immolation , was left on a river of lava to die . Sidious , however , arrived on the planet , and took his apprentice ' s ruined body to Coruscant , where Darth Vader was rebuilt into the figure who was feared , as the Empire ' s most deadly servant , until mere minutes before his death . Prelude . During the Confederacy of Independent Systems ' invasion of the galactic capital , Coruscant , Count Dooku , the Head of State of the Separatist Council and the Confederacy , was executed by the Jedi Knight Anakin Skywalker at the urging of Palpatine , in actuality Dooku ' s master , Darth Sidious . Following this loss , General Grievous , the Supreme Commander of the Separatist Droid Army , became the political leader of the Separatists as well and took control of the Council , which at the time was based on the sinkhole planet Utapau . Grievous ' s first action , under Sidious ' s guidance was to transfer the Council from Utapau to Mustafar : Sidious knew of the impending offensive on Utapau led by General Obi - Wan Kenobi . The Council settled itself into the Klegger Corp Mining Facility . Around this time , an assassination attempt on Sidious led by the renowned Jedi Master Mace Windu resulted in Anakin Skywalker becoming Sidious ' s new Sith apprentice , given the moniker Darth Vader . Vader , believing wholeheartedly in Sidious ' s abilities to save his wife , Padmé Amidala , from death , led the 501st Legion of clone troopers to the Jedi Temple to the Jedi Order . Following the destruction of the Jedi Order , Sidious had no further use for the Separatists . He 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 ( a clear euphemism for their impending slaughter ) . In addition to this , Viceroy Nute Gunray was named Head of State of the Confederacy of Independent Systems , a title which he would hold for a limited time . The assassinations . When Darth Vader arrived at the control bunker on Mustafar , Nute Gunray , San Hill , and the other members of the council welcomed him . At the time , the Separatist leaders were demoralized by their recent defeats in the Outer Rim Sieges , the loss of Count Dooku , General Grievous and their sudden withdrawal from Utapau shortly before the battle . Many of them wanted to sue for peace with the Galactic Empire , formerly the Galactic Republic . However , upon his arrival , Vader immediately closed the doors of the bunker , trapping the Separatist leaders , their aides , and several B1 battle droids within . Engaging in a rampant killing spree , Vader destroyed the battle droids and killed the members of the Neimoidian Gunnery Battalion before looking to his targets . After Vader first slaughtered Denaria Kee , Aito Laff , Po Nudo , and Passel Argente , the remaining Separatists fled . Vader went after them and killed Nank Tun , Cat Miin and Shu Mai . Vader then strode after and killed Tikkes , San Hill , Nudo ' s Aqualish aide , Poggle the Lesser and Aruteous 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 beloved . 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 . Unbeknownst to the Separatists , Sidious was secretly watching the carnage inflicted by his Sith Apprentice as he left his comm link on , just before the Declaration of the New Order . Aftermath . With the death of the Separatist Council , Vader received the order to end the Clone Wars by sending a shutdown signal to the entire Separatist Droid Army and Confederate Navy . Without their droid army and navy , to protect them , the remaining Separatist planets were forced to surrender to the Empire and live under Imperial rule . This action effectively ended all combat operations between the Galactic Empire and the Confederacy of Independent Systems across the galaxy . Before Vader left the planet , his wife Padmé Amidala arrived to question him about his involvement with the massacre at the Jedi Temple on Coruscant . She hadn ' t realized that Obi - Wan Kenobi , Vader ' s former master , had smuggled himself on board her ship . When Kenobi revealed himself to Vader , it looked as if Amidala had brought him to Mustafar to confront him . Believing himself betrayed , Vader choked his wife into unconsciousness . Kenobi also tried to reason with his former Padawan , but without success . Kenobi was forced to fight Vader . Vader was severely injured in the ensuing duel , but was rescued by Palpatine and some clone troopers . However , his condition was so critical that he was forced to spend the rest of his life in a life support suit . After the massacre of their leaders , the Trade Federation and the Techno Union were forced to turn over their assets to the Empire , the former of which attempted a last stand against the Empire , while the Corporate Alliance and the Commerce Guild were quietly dissolved . The InterGalactic Banking Clan , however , survived the catastrophe , though it was much less successful than before . Behind the scenes . This mission was first depicted in , released in 2005 . In the , Vader is depicted fighting his way through the mining facility after killing two aides at the landing platform and battling battle droids and Neimoidian guards . Upon reaching the war room , Vader kills Poggle the Lesser with the room ' s blast door and kills Wat Tambor , two unidentified Neimoidians , and Rune Haako , who pleads for his life before dying . As Nute Gunray attempts to escape in his shuttle , Vader brings it down into the lava below . The depicts Vader as killing each of the Council members in a particularly brutal way , and responding to the Separatists ' pleas for mercy with amusing one liners and witty wordplay . In particular , he responded to Nute Gunray ' s pleas of Sidious ' s promise to leave them " in peace " with the remark , " His transmission was garbled . He promised to leave you in " pieces " . " Also notable is that this version marks San Hill as the first casualty , followed by Poggle , then Shu Mai , then Rune Haako , then Wat Tambor , then Nute Gunray .