Order 66 is usually remembered as the moment the Jedi were wiped out, but there was another side of the Clone Wars that almost never gets talked about: the Separatists. While the clones were turning on the Jedi, the Separatist leaders were still alive on Mustafar, waiting for what they thought was the end of the war.
But they had no idea the war had never truly belonged to them. It belonged to Sidious from the beginning. So what did the Separatists think was happening when Order 66 finally began?
The Separatist Leaders Thought They Had Won
When Order 66 happened, the Separatist leaders were not watching it unfold like the rest of the galaxy. They were hiding on Mustafar, exactly where Darth Sidious had sent them. From their point of view, the war was almost over. Count Dooku was dead, General Grievous was dead, the Jedi were being accused of treason, and Sidious had promised that his new apprentice would come to take care of everything.
That is what makes Vader’s arrival on Mustafar so dark. Nute Gunray does not greet him like an enemy. He says, “Welcome, Lord Vader. We’ve been expecting you.” The Separatist Council believed Vader was there as Sidious’ representative, maybe even to finalize the peace they had been promised.
But they were never partners in Sidious’ plan. They were evidence.
Once Vader arrived, he sealed the room and began killing them one by one. Only then did they understand what was really happening. Gunray’s final plea says everything: “The war is over. Lord Sidious promised us peace…” He still thought there was some kind of deal, some reward waiting for them after helping Sidious tear the Republic apart.
But there was no peace coming for them. Sidious had used the Separatists to create the Clone Wars, weaken the Jedi, frighten the Republic, and justify the rise of the Empire. Once that was done, the Separatist leaders had no purpose left except to disappear.
The Separatist Worlds Were Left With Something Worse Than the Republic
After Vader killed the Separatist leaders on Mustafar, the war basically ended with one command. The droid army was shut down, Grievous was already dead, Dooku was already gone, and the people who controlled the Separatist movement had just been erased. To the galaxy, it looked like the Republic had finally defeated the Separatists. But the truth was much darker than that.
A lot of worlds joined the Separatist cause because they were tired of the Republic. They believed the Senate was corrupt, that the Core Worlds had too much power, and that independence was the only way out. But after Order 66, those worlds did not get freedom. They did not get the future they thought they were fighting for. They were swallowed by the Empire.
We even see the aftermath later with worlds like Raxus in The Bad Batch. Raxus had been the Separatist capital, but after the Clone Wars, it was under Imperial control like everyone else. Senator Avi Singh fought to leave the Republic, only to realize the Empire was even worse.
Another example is Desix. Governor Tawni Ames still saw her world as independent, because Desix had already separated from the Republic during the Clone Wars. But the Empire did not care about that. It sent its own governor, expected Desix to obey, and treated Ames’ resistance like another Separatist problem that needed to be crushed. So even the worlds that still tried to hold onto their independence learned the same thing: the Empire was not there to negotiate.
