The leader of the Lurmen, Tee Watt Kaa, refuses to shelter the Jedi from arriving Separatist forces, fearing that such an action would unnecessarily bring his neutral people into the war. Ahsoka, Aayla, the wounded Anakin, and the rest of the clones respect their wishes as they don't want to jeopardize the village with their presence, so they have to retreat into the wilds of the planet. Separatist Neimoidian General Lok Durd arrives to test a devastating weapon, which they plan to use on the Lurmen! Ultimately, the villagers have to decide whether they will lay down to the Separatists or fight with the Jedi to defend their village.

Anakin Skywalker and Obi-Wan Kenobi lead Republic forces in an attempt to defeat the droid armies and free the planet of Christophsis from the Separatist siege. When the Republic is ambushed and forced to retreat, it becomes clear that someone in their midst has set them up. The Jedi believe this infiltration is a Sith-backed operation and go behind enemy lines to investigate. Meanwhile, Captain Rex and Commander Cody set out to uncover the traitor amongst them.

The Jedi Council suspects that Senator Rush Clovis, an InterGalactic Banking Clan delegate and former colleague of Padmé Amidala, may be working for the Separatists. Against Anakin's wishes, the Council asks Padmé if she would accompany Rush to Cato Neimoidia to uncover any clues regarding the Senator's true allegiances. Padmé agrees, feeling that her past relationship with the Senator -- which for a time had been romantic until she ended it -- might give her an advantage in the investigation. Fending off Anakin's jealousy, as well as an attempt on her life by Neimoidian Lott Dod, Padmé successfully reveals Clovis to be conspiring with the Separatists to build a military droid factory on Geonosis.

After a battle to destroy a new droid factory on Geonosis, Jedi Master Luminara Unduli disappears while tracking Poggle the Lesser. Obi-Wan and Anakin lead a platoon of clone troopers in search of her. Following her trail, our heroes descend deep into the lair of Karina the Great. To their horror, they learn that the hive is alive and teeming with undead defenders. Apparently, Karina can reanimate and control her subjects. Will Obi-Wan and Anakin overcome Karina's undead horde and find Luminara before it's too late?

Medical supplies are desperately needed for a crucial Republic battlefront. While the Jedi Knights transport Poggle the Lesser as a prisoner to Coruscant, the Padawans Barriss Offee and Ahsoka Tano are dispatched to escort the medical frigate to its destination. When Geonosian brain worms take control of the clone troopers aboard their supply ship, Ahsoka and Barriss must battle to stop the vessel from unleashing the deadly plague upon the galaxy.

Anakin, Obi-Wan, and Ahsoka crash on Felucia and seek aid from the local spice farmers only to learn that the farmers are the ones who are in real need. Beset by Hondo Ohnaka and his band of pirates who plan to steal their crop, the farmers have contracted four deadly bounty hunters to protect their wares. In an unlikely partnership, the Jedi must work with the farmers' hired guns to beat back Hondo and his brigands.

Per Palpatine's order, Republic forces transport a fearsome Zillo Beast back to Coruscant for scientific study. Eager to extract the beast's secrets for military gain, Palpatine orders his lead scientist to examine, and subsequently, kill the monster. Filled with pain and anger, the Zillo Beast escapes from the lab and begins devastating the city. Soon, Anakin, Padmé, and Palpatine find themselves pursued by the beast while the Jedi fight to contain it.

Determined to kill Jedi Master Mace Windu, young Boba Fett poses as a clone cadet and sneaks aboard a Jedi cruiser to plant a bomb in Windu's quarters. But Boba's plan goes awry when the blast fails to kill Mace and, suddenly, every clone aboard is looking for the saboteur. Boba destroys the ship's reactor to create a distraction and, soon, the entire cruiser begins to break apart. Unaware that Boba is the culprit, Boba's new cadet comrades save his life but is he too obsessed with revenge to do the same for them?

Cad Bane has broken Ziro the Hutt out of prison. The Hutt Council demands that Ziro tell them where he's hidden vital -- and incriminating -- information: a journal detailing the criminal activities of the Hutt families. Ziro makes another daring escape with the help of his estranged (and strange) lover, Sy Snootles. Bane is back on the Hutt's trail -- but he's not the only one. The Jedi Obi-Wan Kenobi and Quinlan Vos need to find him too. A chase through the swamps of Nal Hutta leads the pursuers to Ziro's enormous mother, Mama the Hutt, who points them to Teth. It is here, in the secret grave of Ziro's father, that the fugitive Hutt has hidden the diary. When he retrieves it, Snooty reveals her true spots. She's a deadly woman scorned and a bounty hunter for hire!

A mysterious force draws Anakin, Obi-Wan and Ahsoka to a distant planet, and its inhabitants -- a family of exceptionally powerful Force-wielders -- in an attempt to determine whether Anakin is truly the Chosen One. The patriarch of this family, known only as the Father, has spent ages maintaining the balance between his Daughter, who is strong with the light side of the Force, and his Son, who aligns with the dark. The Father reveals his days are numbered, and he seeks Anakin to take his place as the fulcrum of this balance. A series of tests proves that Anakin is capable of controlling both offspring, as the Father does, but Skywalker refuses to take the Father's place.

The Jedi remain stranded on Mortis, and the Son, aligned with the dark side of the Force, renews his efforts to convert Anakin as the Jedi prepare for a decisive confrontation. Anakin is stunned by images of his dark future. The Son promises him the power to avert this destiny. The Father recognizes that the Son has broken the rules of time. He wipes Anakin's memory of these future visions, and steals the Mortis Dagger to end the conflict. The Father impales himself, thus preventing the Son from stealing his power. The Son, stunned by this, is run through by Anakin. With all three Force-wielders destroyed, the imbalance in the Force disappears on Mortis. The three Jedi are transplanted back to the galaxy proper, apparently at the moment that they disappeared.

After their ship and only way off the planet is destroyed, Anakin and Obi-Wan must lead the escaped prisoners across Lola Sayu's perilous landscape as Plo Koon commands a task force of four cruisers and their fighters through the Separatist defenses in a daring rescue. Even Piell is ravaged by anooba tracking beasts, but before he dies, he passes on his Nexus Routes coordinates to Ahsoka. When the survivors return to Coruscant, Ahsoka knows half the intel, and refuses to disclose it to anyone but the Jedi Council, while Tarkin refuses to hand over his half to anyone other than the Chancellor.

C-3PO and R2-D2's bizarre caper continues. Forced to escape a Separatist attack in a Y-wing fighter, the droids visit the world of the Patitites, the odd planet Balnab, and the inside of a pirate warship where they are forced to fight in a gladiatorial arena.

When Anakin is forced to temporarily turn over command of his clone troopers to a new commander, the Jedi Pong Krell, tensions begin to run high as the clones are assigned with a very deadly mission to take the capital of Umbara.

Count Dooku is determined to have revenge against the Nightsisters of Dathomir after their betrayal. General Grievous launches an all-out droid attack against the magic-wielding witches, and Mother Talzin and Asajj Ventress lead the defense with all the dark powers at their command.

Fueled by vengeance and rage, the newly reunited brothers Savage Opress and Darth Maul spread terror and violence across the galaxy. As the Sith brothers forcibly recruit Hondo Ohnaka and his pirates, Obi-Wan Kenobi and Adi Gallia chase them down, leading to a deadly confrontation.

Supervised by Ahsoka, the Onderon rebels infiltrate the capital and carry out a series of strikes on targets throughout the city. As the Separatist-aligned king comes under increasing pressure to deal with the growing rebellion, the rebels choose a new leader.

In a nearly vacant town, R2-D2 and his team find a clone commando suffering from amnesia.

Rush Clovis' deal with the Separatists backfires and brings war to the banking world of Scipio.

The peaceful world of Bardotta and its mystic ways are threatened by an ancient prophecy, and its top spiritual leaders have vanished. Queen Julia of Bardotta calls for help from her most trusted friend in the Senate, Jar Jar Binks. Recognizing the importance of Bardotta's spiritual balance, the Jedi Council sends Mace Windu to accompany Binks and investigate.

After many grueling trials, Yoda next travels to the ancient Sith home world of Moraband, where he must face an ancient evil determined to rule the galaxy.

Obi-Wan and Anakin investigate a mysterious death of a Jedi Master on Utapau, and uncover a secret Separatist weapons deal the likes of which they have never seen before.

Rex, Anakin, and the Bad Batch look to uncover the truth surrounding a mysterious Separatist signal.

Rafa lands a dangerous job running spice — and she needs Ahsoka and Trace's help.