Darth Sidious orders Lord Tyrannus to eliminate Asajj Ventress, lest her becoming too powerful. But Ventress escapes and manages to make her way back to her home planet of Dathomir, vowing revenge on Count Dooku.
Count Dooku accepts Mother Talzin's offer to present him with a warrior from the same tribe as Darth Maul. However, Talzin and Asajj Ventress pick and train the warrior and use Nightsister magic to bend him to their will.
Anakin, Obi-Wan and Ahsoka investigate a mysterious transmission and find a gateway to a hidden planet called Mortis. There reside three powerful Force-wielders who haunt all three Jedi with visions and mean to find out of Anakin really is the Chose One.
Before the Jedi can leave Mortis, the Son abducts Ahsoka and infects her with the Dark Side. While Anakin faces his Padawan, the Daughter reveals to Obi-Wan the only weapon that can defeat her brother: the Dagger of Mortis.
The water planet Mon Calamari is on the brink of civil war. Republic Senator Amidala and her Jedi protector Anakin Skywalker take the side of the Mon Cal, while Separatist representative Riff Tamson spurs on the Quarren.
During an assault on the shadowy world of Umbara, General Skywalker is called back to Coruscant. He has to relinquish command of the 501st legion to legendary Jedi Master Krell, who turns out to have a low opinion of Clones.
The Separatists support Zygerrian slavers in taking over a Togruta colony on the neutral planet Kiros. Anakin and Ahsoka race to defuse a series of bombs while Ob-Wan faces the Zygerrian leader, Darts D'Nar.