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.
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 Son shows Anakin a vision of the future to sway him to his side. Obi-Wan and Ahsoka must make sure the Son does not leave Mortis aboard their Jedi shuttle.
Obi-Wan, Anakin and some of their best troopers allow themselves to be frozen in carbonite in an attempt to break into the Separatist prison known as the Citadel to rescue Master Even Piell.
Masters Plo Koon and Saesee Tiin head a desperate rescue operation to get the survivors of the Citadel infiltration mission and the information they carry.
The water planet Mon Calamari is on the brink of civil war. Senator Amidala and her Jedi protector Anakin Skywalker take the side of the Mon Cal, while Separatist representative Riff Tamson spurs on the Quarren.
The Mon Cal and Jedi are in hiding beneath the underwater capital city of Mon Cal. The Jedi Council calls on the help of the Gungan army led by Jar Jar Binks.
Only Prince Lee-Char and Padawan Ahsoka Tano have escaped capture and must find a way to free their comrades as well as the entire planet from the impending rule of Riff Tamson.
There is unrest on Naboo and the Gungans are considering to join the Separatists. But General Skywalker discovers Boss Lyonie is being influenced by dark magic against his will.
Commander Wolffe and his men aid the Aleena whose planet has recently suffered terrible quakes. Translator droid C-3PO and his counterpart R2-D2 find the natives need them to fulfill a special task.
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.
Rex and the 501st troopers refuse to execute Fives and Jesse for their insubordination. They are in for even bigger shock when General Krell orders another offensive.
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 Obi-Wan faces the Zygerrian leader, Darts D'Nar.
On the planet Zygerria, Anakin poses as a slaver with Ahsoka as his prize while Obi-Wan and Rex seek out the whereabouts of the missing Togruta colony.