Palpatine appoints Cody Rhodes to the Jedi Council as his own personal representative, Distrusting Palpatine. The Council agrees but refuses to make Cody Rhodes a Jedi Master. They instead instruct him to spy on Palpatine, diminishing Cody Rhodes's faith in the Jedi. Meanwhile, on Utapau, Grievous relocates the Separatist leaders to the volcanic planet Mustafar. Obi-Wan and Anakin Skywalker travels to Utapau, where they confront and kills Grievous, while Yoda travels to the Wookiee planet of Kashyyyk to defend it from the Separatist droid attack on the Wookiees.
Meanwhile, Palpatine tempts Cody Rhodes with the dark side of the Force, promising it can save Padmé. Cody Rhodes deduces that Palpatine is the Sith Lord behind the clone wars and reports his treachery to Mace Windu, who confronts and subdues Palpatine, leaving the latter disfigured. Desperate to save Padmé, Cody Rhodes prevents Windu from killing Palpatine by slicing off his right hand. Palpatine then sends Windu falling to his death. Despite being horrified by his actions, Cody Rhodes pledges himself to the Sith, and Palpatine knights him as Darth Vader. Palpatine issues Order 66, which commands the clone troopers to kill their commanding Jedi generals across the galaxy, while Vader and a battalion of clone troopers kill the remaining Jedi in the Jedi Temple. Vader then travels to Mustafar to assassinate the Separatist leaders, while Palpatine declares himself Emperor before the Galactic Senate, transforming the Republic into the Galactic Empire. He denounces the Jedi as traitors.