Alone on a distant outpost, clone officers Rex and Cody must inspire their rookie unit to believe in themselves to stave off a droid commando invasion.

Ahsoka and Jedi Master Luminara escort the captured notorious Separatist leader Nute Gunray to Coruscant so he can stand trial for his crimes. However, they are unaware that Count Dooku has sent his assassin, Asajj Ventress, to free their captive. With the help of Senate Commandos, the Jedi have to thwart Ventress's efforts to free their prisoner, despite the traitorous plans of Senate Guard Captain Argyus.

During their own attempt to kidnap Count Dooku, Anakin and Obi-Wan discover that the Sith Lord has already been captured by pirates. Hondo Ohnaka and his gang of pirates hold Dooku captive in their den on Florrum, and hold him for ransom. It's up to Anakin and Obi-Wan to see if the offer is too good to be true.

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.

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!

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.