Fives continues to push for answers regarding the mystery of the clone contamination and secures an audience with Supreme Chancellor Palpatine. But the situation quickly collapses when Fives is accused of attacking the Chancellor, and he must flee deep into the Coruscant cityscape while pursued by fellow clone troopers.

A Jedi mission finds a lightsaber belonging to the long-dead Master Sifo-Dyas, prompting Yoda, Obi-Wan Kenobi, and Anakin Skywalker to begin an investigation into his decade-old disappearance. This sparks Darth Sidious to order Darth Tyranus to clean up any loose ends that may lead the Jedi to discover the truth of the Sith conspiracy.