Anakin and Obi-Wan have been duped and are being held for ransom along with Count Dooku by the pirate chief Hondo Ohnaka and his second-in-command, Turk Falso. While Anakin, Obi-Wan and Dooku unsuccessfully attempt to escape, the Republic sends the ransom via a special envoy, including Representative Jar Jar Binks. When Falso tries to steal the ransom from his boss by shooting down the shuttle, the only survivors are a squad of clones and Jar Jar, who as the most senior officer alive, has to take charge of the mission. It becomes a race against time as Jar Jar rushes to deliver the ransom to take custody of Dooku and save the Jedi.

Anakin and Ahsoka arrive at a pitched sky battle to help besieged Jedi General Aayla Secura. Anakin is gravely injured in the fight. Aayla and Ahsoka, along with the now-wounded Anakin, Rex, and the surviving clones, crash land on the uncharted grass-covered planet, Maridun. Forced to leave Anakin behind in order to save him, Aayla teaches Ahsoka why the Jedi have no personal attachments. They make their way to a Lurmen village. Their ruler, Tee Watt Kaa, explains that they're pacifists in this war and are not aligned with either side. Hesitant to have anything to do with the Jedi, Tee Watt Kaa agrees to help save Anakin's life.

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.

Arriving on the desolate ice world of Orto Plutonia, Anakin Skywalker and Obi-Wan Kenobi investigate the disappearance of a clone security force stationed on a remote outpost. The Jedi, accompanied by Senator Riyo Chuchi and Chairman Cho of the nearby moon of Pantora, soon discover their clone troopers were attacked by a tribe of furry natives known as the Talz. Fierce beast-riding warriors, the Talz are very territorial and only want to be left alone. The Jedi manage to negotiate peace with the Talz chieftain, Thi-Sen, when greedy Chairman Cho breaks it by insisting the planet and the Talz are under his power. The resulting conflict escalates into war between the senator led clones and the Talz, with the Jedi in the middle.

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 Republic discovers a Separatist bio-weapon lab hidden on the planet of Naboo. Rather than wait for help, Padmé; explores the lab with Jar Jar. Anakin, Ahsoka, Rex, and Obi-Wan arrive and follow after her. They find that the Senator is being held captive by the sinister Dr. Nuvo Vindi. The mad scientist has been developing a lethal virus for the Separatists. Vindi threatens to set off a bomb and release the virus!

Even though the lab has been shut down, Dr. Vindi manages to activate the dreaded Blue Shadow Virus, infecting Ahsoka, Padmé, and many clone troopers. The plague is fatal within 48 hours. Anakin and Obi-Wan must travel to the mysterious planet, Iego, to secure the only known antidote to the sickness. Anakin and Obi-Wan arrive on the mysterious planet to find its population living in fear of a mysterious force that has been killing anything that tries to leave their world. With the help of Jaybo Hood, a clever Iegoan boy, Anakin and Obi-Wan must solve the planet's mystery before they can leave, and before everyone infected with the Separatist virus dies!

Ryloth, home world of the Twi'lek people, has been subjected to military occupation by the droid army of the Separatists, and surrounded by a blockade of Trade Federation battleships. While launching a surprise attack against the blockade, Ahsoka disobeys Anakin's orders and ends up losing most of her squadron. Even though she's emotionally rocked by this failure, Anakin helps her learn to persevere, placing her in charge of another risky attack.

With the space blockade around Ryloth destroyed, Obi-Wan Kenobi must lead a small clone force into a droid occupied town to sabotage their anti-aircraft guns. Obi-Wan's mission is complicated when he learns the town's inhabitants are being used as living shields. A pair of clones in his platoon forges an unlikely friendship with a refugee Twi'lek girl, Numa, who's been orphaned by the war. Through their relationship with her, the clones begin to understand the real cost of the war...

The battle for the Twi'lek homeworld of Ryloth rages as the Republic attempts to drive off the occupying droid army led by Separatist Leader, Wat Tambor. With his forces stretched thin, Mace Windu must convince Twi'lek freedom fighter, Cham Syndulla, to help him save the capital city from the droids' destruction. Initially, the Twi'lek hero is hesitant to aid Mace, but ultimately realizes the Jedi can be trusted and joins with him to liberate the city -- and ultimately the planet -- in the climactic battle.

In an attempt to force the release of the crime lord Ziro the Hutt from prison, bounty hunters seize control of the Senate Building and hold members of the Senate hostage. Cad Bane, the leader of the operation, with the help of bounty hunter Aurra Sing, issues his demands to Chancellor Palpatine who has no choice but to meet his request. Unbeknownst to the hunters, Jedi Knight Anakin Skywalker is loose in the Senate Building.