Anakin and Ahsoka travel to the planet Devaron in pursuit of Cad Bane, who has stolen a Jedi holocron. Bane has captured Jedi Master Bolla Ropal, keeper of the Kyber crystal, which will reveal data on every known Force-sensitive child in the galaxy when combined with the holocron. Failing to force Ropal to open the holocron, Bane needs another Jedi. Capturing Ahsoka, the bounty hunter forces Anakin to open the holocron to save his Padawan. The holocron's secrets revealed, Bane attempts an escape, but appears to be killed by a clone. Anakin, however, still senses Bane's presence in the Force...

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.

Anakin, Obi-wan, and Ki-Adi-Mundi lead an invasion to stop Poggle the Lesser and the Geonosians from rebuilding their droid army. Things go terribly awry when Geonosian forces shoot down the Republic ships, which crash off-course. Under mounting pressure to accomplish their mission, Anakin, Obi-Wan, and Ki-Adi-Mundi each have their own set of challenges to overcome -- hordes of enemy troops, deadly traps, unforgiving terrain, and a massive energy shield.

Anakin, Ahsoka, Luminara Unduli and her Padawan, Barriss Offee, lead a mission to destroy a droid factory on Geonosis. But Poggle the Lesser has other plans as he deploys his newest weapon, the indestructible super tanks. Desperate to accomplish their mission before the foundry comes online, the Jedi devise a daring plan in which Anakin and Luminara will act as decoys, diverting the super tanks, while Ahsoka and Barriss infiltrate the plant via a labyrinth of catacombs beneath the city. The plan is risky. The stakes are high. It's their only option, but are the Padawans up to the challenge?

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.

Jedi Master Eeth Koth is taken hostage and tortured by General Grievous. Anakin Skywalker, Obi-Wan Kenobi and Adi Gallia devise a daring rescue plan, but they soon realize the General has a plan of his own. The Jedi Knights and the Separatist general try to outmaneuver each other in a ship-to-ship and hand-to-hand battle high over the planet Saleucami.

General Grievous is shot down over Saleucami and crash lands in the wilderness. Obi-Wan leads an expedition to find the droid general. Rex is injured during the search, and must recover in a local farmer's barn, but he is shocked to discover the farmer is a clone deserter.

During an assignment in the Coruscant underworld, a wily pickpocket steals Ahsoka's lightsaber. Ahsoka enlists the help of an ancient Jedi, Tera Sinube, to track down her weapon and reclaim her honor.

Alarming rumors about the peace-abiding Duchess Satine of Mandalore prompt Obi-Wan to investigate the secluded planet. Satine wants to keep Mandalore neutral in the Clone Wars, but the actions of a violent splinter group -- Death Watch -- threaten to push the planet towards war.

Duchess Satine travels from Mandalore to Coruscant on a diplomatic mission, with Obi-Wan Kenobi, Anakin Skywalker and a team of troopers to defend her. As her luxurious starship, Coronet, makes its way through hyperspace, the Jedi must stop several assassination attempts, and Anakin discovers that Obi-Wan and the Duchess have a history together.

On Coruscant, word reaches Duchess Satine that Death Watch is mobilizing, sparking a pre-emptive Republic invasion. On the run from Republic authorities, Satine and Obi-Wan set off to discover the group's true motives.

When Senator Onaconda Farr dies under suspicious circumstances and the local Inspector appears incompetent, Padmé; sets out to find the person who poisoned her mentor. Following a trail of clues, Padmé and Bail Organa delve into a dangerous world of backstabbing, lies, and secrets controlled by the powerful Senators Mee Deechi and Halle Burtoni. Padmé's search forces her to risk her career and ideals but the true identity of the assassin is even more destructive than she could imagine.

A Separatist blockade surrounds Christophsis. Anakin's fleet is tasked with deploying relief supplies to the surface but they are massively out-gunned and out-maneuvered by the skillful Admiral Trench. Obi-Wan arrives and unveils the Republic's new weapon: a stealth ship. The stealth ship is the last hope at besting the cunning Separatist fleet commander and aiding the battered people of Christophsis.

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.

Desperate to turn the tide of a fierce battle on Malastare and win a strategic alliance with the Dugs, Chancellor Palpatine orders the Jedi to drop the Republic's newest super-weapon, an untested electro proton bomb. Unfortunately, the bomb's blast awakens an ancient and fearsome Zillo Beast, a monster of legendary size and ferocity. Now the Jedi must contain this deadly creature despite the interference of the bloodthirsty Dugs, who have their own agenda.

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?

Boba Fett and his band of bounty hunters lead Anakin and Mace into a deadly trap on Vanqor. It's up to R2-D2 to journey back to Coruscant and warn the Jedi of their brethrens' peril. Battling beast and bounty hunter along the way, the trusty droid finally communicates his warning to Ahsoka and Plo Koon, who rush to Vanqor to save Mace and Anakin from a fiery death.

Following a nefarious attempt to murder Anakin Skywalker and Mace Windu on Vanqor, Boba Fett and Aurra Sing go into hiding. Jedi Master Plo Koon and Ahsoka Tano set out to capture the bounty hunters. While combing through the lower depths of the Coruscant underworld, Plo and Ahsoka finally learn that Fett and his group are hiding out on Florrum. In a dramatic showdown, Fett is abandoned by Aurra Sing, leaving young Boba angry and bitter in Republic custody.