During the Clone Wars, the Confederacy of Independent Systems' Separatist Council maintained a critical war room. This strategic location was situated within the Klegger Corp Mining Facility, found on Mustafar. It was to this very room that the leaders of the Confederacy of Independent Systems retreated to as the Clone Wars reached its conclusion.
This war room was an integral part of a clandestine command center. Constructed as an addition to the Klegger Corporation's mining complex, it served as a fortified shelter for the Separatist Council. The spacious chamber featured a pair of large holoprojector tables at its center, designed in the shape of the Confederacy of Independent Systems' emblem. Control panels and screens lined the walls, displaying status updates from the mining facility, monitoring approaching vessels, and providing remote control over the facility's shield systems. Three doorways punctuated the walls: one leading to a hallway that connected to a landing platform, another providing access to a conference room, and the last opening to a walkway overlooking the mining operations below. The room also had a control panel capable of locking the doors, as well as internal automated defense systems.
In the early days of the Separatist Movement, the Separatist Council foresaw the need for a fallback location should their ambitions falter. Mustafar was selected as the site for their secret bunker, its inhospitable environment seen as a natural defense. Under the guise of a mining operation, the Techno Union, through its subsidiary Klegger Corporation, constructed a secret droid factory. Within this facility, the Separatists established their bunker, with the war room at its heart.
As 19 BBY arrived, marking the end of the Clone Wars, General Grievous dispatched the Separatist Council to their Mustafar bunker. They were guarded by OOM-series security droids and the [Neimoidian Gunnery Battalion]. The council convened in the war room, where they received a communication from Sidious. He informed them that his apprentice, Darth Vader, was en route to reward them for their contributions to the Clone Wars. However, Sidious had secretly ordered Vader to assassinate them. Soon after, Vader arrived and was guided to the war room by mouse droids. The Separatists eagerly greeted him, but Vader sealed the room's doors, destroyed the control panel using the Force, and then proceeded to massacre the council, the security droids, and the Neimoidian Gunnery Battalion. Although the room's automated defenses were activated, they proved ineffective against Vader. Sidious maintained the connection, listening to the entire gruesome event.

Following the massacre, Vader contacted Sidious, who instructed him to transmit a message to the Trade Federation ships, ordering the immediate deactivation of all remaining droid units. Vader complied, and noticed on one of the war room's screens that the ship carrying his wife, Padmé Amidala, was approaching. Vader went outside to meet Amidala, only to discover that his former master, Obi-Wan Kenobi, had secretly boarded the ship with the intention of killing Vader. A duel ensued between the two, leading them into the war room and briefly into the adjacent conference room before returning to the war room. At one point, their simultaneous Force pushes resulted in both being thrown to opposite ends of the room. Vader quickly recovered and leaped across one of the holoprojector tables, attempting to strike Kenobi. The Jedi blocked the lightsaber strike, redirecting it into the control board beside him, inadvertently disabling the facility's shields. The two then destroyed the locking mechanism of the door to the walkway above the mining operations, and it opened behind them, which they proceeded through.