Mission to Mustafar

Back in 19 BBY, following the death of Count Dooku at the hands of Jedi Knight Anakin Skywalker during the Battle of Coruscant, General Grievous rose to become the public figurehead of the Confederacy of Independent Systems. Under orders from the Sith Lord Darth Sidious, Grievous relocated the Separatist Council, then situated on Utapau, to the Klegger Corp Mining Facility on Mustafar, secretly intending to assassinate them, as they had outlived their usefulness to him. Grievous complied, informing the council of their destination before they boarded a transport. Immediately following this, the Battle of Utapau erupted, resulting in Grievous's death at the hands of Jedi Master Obi-Wan Kenobi, leaving the Separatist Council as the only remaining public leaders of the Separatists. Upon arriving on Mustafar, they received a communication from Darth Sidious, who instructed them to initiate the shutdown of their droid armies.

After Skywalker's betrayal of the Jedi, his descent into the dark side, and his oath to Darth Sidious, transforming into Darth Vader, he was dispatched to Mustafar following Operation: Knightfall with the purpose of eliminating the Separatist Council. As Vader approached the facility – remotely disabling its air defenses in the process – the Separatists and their aides had assembled in its war room, guarded by soldiers from the Neimoidian Gunnery Battalion and OOM security battle droids. Sidious reestablished contact with the council, inquiring whether the droid armies' shutdown was complete, to which Trade Federation Viceroy Nute Gunray confirmed its completion an hour prior. Sidious then deceived the council, informing them that they would be rewarded for their involvement in the Clone Wars and that his new apprentice was arriving to bestow said reward.

Upon landing, Vader instructed his astromech droid R2-D2 to remain with his starfighter while he proceeded into the facility. Two nearby Mustafarians witnessed his arrival. As Vader was escorted to the council by Mouse droids, the Separatists stood around conversing and observing the movements of clone troopers on holograms.

Upon Vader's entry into the war room, the Separatists hastened to greet him, with Gunray and InterGalactic Banking Clan Chairman San Hill leading the way. Vader responded by sealing the room's doors and destroying the control panel using the Force, effectively trapping the Separatists inside. Hill, recognizing Vader as Skywalker, recoiled in horror as Vader ignited his lightsaber and impaled him through his three hearts, resulting in his immediate death.

With Hill deceased, Vader then turned his attention to two members of the Neimoidian Gunnery Battalion, Gap Nox and Fame Drimal, who were positioned near the entrance, and swiftly eliminated them. Embarking on a frenzied killing spree, Vader traversed the room, slaughtering members of the council, their aides, and additional members of the Neimodian Gunnery Battalion, while also dismantling the security battle droids. Despite the war room's automated defense systems, Vader successfully defended against them. As he moved through the room, he killed the Magistrate of the Corporate Alliance, Passel Argente and his aide Denaria Kee; Ando system Senator Po Nudo, and his aides, Nank Tun and another Aqualish; Mon Calamari system Senator Tikkes; Cat Miin, the aide of the Presidente of the Commerce Guild, Shu Mai; and several Trade Federation advisors, which included Aruteous Gunnay and Aito Laff.

Vader then turned his attention to the Archduke of Geonosis, Poggle the Lesser, who attempted to defend himself with his cane, and Mai, who pleaded with Vader, claiming that they were promised a handsome reward, to which he mockingly stated that he was their reward and questioned that she didn't find him handsome before slicing her head off.

Gunray, along with his Lieutenant Rune Haako and Foreman Wat Tambor of the Techno Union, sought refuge in a nearby conference room. Vader pursued them, dragging his lightsaber along the wall. Haako stumbled over a chair, and Vader swiftly caught up to him, disregarding the Neimoidian's pleas, and slashed him across his body. Vader then discovered Tambor clawing at the conference room's viewports. Tambor offered Vader anything in exchange for his life, but Vader seized his shoulder and plunged his lightsaber through his body, before severing his arms and head, sarcastically thanking him afterward.

Gunray, now the sole surviving member of the Separatist Council, retreated back into the war room, only to be intercepted by Vader, who jumped in front of him. Gunray desperately pleaded with Vader, asserting that the war was over and Sidious had promised them peace, to which Vader retorted that his transmission was garbled and Sidious actually said they'd be left "in pieces," before slashing him across his chest, killing him. Unbeknownst to the Separatists, Sidious had maintained the connection and observed the entire slaughter.

Vader stepped outside the war room and stood on a balcony overlooking the lava below, gazing at the sky, a tear tracing its path down his cheek as he contemplated his transformation into a Sith Lord. He then reentered the facility and peered through the viewports of the conference room, contemplating the galaxy and his aspirations to rule it. Upon returning to the war room, he contacted Darth Sidious and reported the Separatists' demise. Sidious then commanded Vader to transmit a message to the Trade Federation's ships, instructing all remaining droid units to immediately shut down. Vader complied, effectively ending the Clone Wars. As he issued the shutdown order, he noticed the starship of his wife, Padmé Amidala, approaching the facility. Upon exiting to greet Amidala and inquire about her presence, Vader spotted Kenobi, his former master, standing on the entry ramp of the ship, having secretly boarded without Amidala's knowledge.

Vader, under the false impression that Amidala had brought Kenobi to assassinate him, Force choked her and engaged Kenobi in a duel, their battle spanning the war room, the balcony, and the rest of the facility.

Following the massacre of their leaders, the Trade Federation and the Techno Union were compelled to surrender their assets to the Empire, with the former staging a last stand against the Empire, while the Corporate Alliance and the Commerce Guild were quietly dissolved. The InterGalactic Banking Clan, however, weathered the catastrophe, albeit with diminished success compared to its former state.

This mission was initially portrayed in Star Wars: Episode III Revenge of the Sith, which premiered in 2005.

In the DVD commentary for Revenge of the Sith, George Lucas revealed that the interwoven scenes of the Mission to Mustafar and the Declaration of a New Order were a tribute to the christening and assassination sequence in the 1972 mob classic film The Godfather, directed by his friend Francis Ford Coppola.

In the Revenge of the Sith video game, Vader is depicted battling 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 Revenge of the Sith novelization 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.