One of Darth Vader's first missions in Star Wars: Episode III – Revenge of the Sith saw him head to Mustafar to end the threat of the Separatists, but he failed in this mission. Palpatine’s grand scheme for transforming the Republic into an Empire needed to be executed carefully, and it was crucial for each event to occur in order. First, before they realized something was amiss, the Jedi were wiped out through Order 66. With his biggest enemy eliminated, Palpatine was free to end the Clone Wars any way he chose. Since he played both sides from the beginning, he chose to disband the Separatists to strengthen the Republic.
The Separatists only existed to keep the Jedi occupied while Palpatine continued to gain power, and their leaders unknowingly served their purpose to the end. Palpatine promised them peace, but couldn’t risk keeping them around as a potential threat. Instead, Vader destroyed them and the Separatist droid army as well. Palpatine used the decimation of the Separatists as a cause for celebration in the Republic, which distracted most of the public from realizing he had seized almost all the power. But, while Vader succeeded in slaughtering the final Separatist leaders, he failed to truly fulfill the other part of his mission.
