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.
Lux Bonteri disrupts a peace conference between Seperatist and Republic representatives on Mandalore. Intent on safeguarding him, Ahsoka becomes involved in Lux's plan to take revenge on Count Dooku for his mother's death.
Obi-Wan fakes his own death and goes undercover as his own 'killer', Rako Hardeen, so he can infiltrate Moralo Eval's plot to kidnap Chancellor Palpatine.
Disguised as Bounty Hunter Rako Hardeen, Obi-Wan Kenobi is on the run with criminal mastermind Moralo Eval and Cad Bane. But their partnership is on thin ice and Anakin and Ahsoka are in hot pursuit.
Count Dooku challenges eleven bounty hunters to survive several deadly levels devised by Moralo Eval. The winners will participate in the plot to kidnap Chancellor Palpatine on Naboo.
Cad Bane leads Dooku's team of bounty hunters, including a disguised Obi-Wan, in a plot to kidnap the Supreme Chancellor during the Festival of Lights on Naboo.
Asajj Ventress returns to Dathomir to become a true Nightsister. But then Count Dooku orders General Grievous to wipe out Mother Talzin and her entire clan of witches.
Asajj Ventress joins a group of bounty hunters led by Boba Fett. Their mission is to deliver a box with unknown cargo to the leader of the planet Quarzite.
Mother Talzin restores Darth Maul's sanity and gives him a better pair of mechanical legs. Now Maul wants revenge on Obi-Wan Kenobi and lures the Jedi to the remote planet of Raydonia.