Lurmen-lederen, Tee Watt Kaa, nægter at skjule Jedi'erne fra seperatisternes styrker af frygt for, at en sådan handling unødigt ville tvinge hans neutrale folk ind i krigen. Ahsoka, Aayla, den sårede Anakin og resten af klonerne respekterer deres ønsker og vil ikke bringe landsbyen i fare ved deres tilstedeværelse, så de trækker ud af byen og ind i planetens vildnis. Den neimodianske seperatist-general Lok Durd ankommer for at afprøve et altødelæggende våben, som de planlægger at bruge mod Lurmen-folket! Til sidst bliver landsbyenboerne nødt til at beslutte, om de vil ligge under for seperatisterne eller kæmpe med Jedi'erne for at beskytte deres landsby.

Anakin Skywalker og Obi-Wan Kenobi leder en republikansk styrke i et forsøg på at besejre droidehæren og befri planeten Christophsis fra seperatisternes belejring. Da de falder i baghold og er tvunget til at trække sig tilbage, bliver de klar over, at de er blevet forrådt af én af deres egne. Jedi'erne mener at indfiltrationen er en Sith-støttet operation og drager ind bag fjendens linier for at undersøge sagen. Imens forsøger kaptajn Rex og kommandør Cody at finde frem til forrædderen iblandt dem.

Jedi-rådet mistænker senator Rush Clovis, som er den intergalaktiske bankklans delegerede, for at samarbejde med seperatisterne. Imod Anakins ønske, beder rådet Padmé om at følge Rush til Cato Neimoidia for at afdække spor om senatorens sande loyalitet. Padmé accepterer rådets ønske baseret på fornemmelsen af, at hendes tidligere forhold til senatoren -- som for en stund var romantisk, indtil hun afsluttede det -- kan give hende en fordel i efterforskningen. På trods af Anakins jalousi samt et mordforsøg fra neimoidianen Lott Dod, afslører Padmé med succes Clovis i at samarbejde med seperatisterne for at bygge en militær droidefabrik på Geonosis.

Efter slaget, der ødelagde en ny droidefabrik på Geonosis, forsvinder Jedi Master Luminara Unduli under forfølgelsen af Poggle the Lesser. Obi-Wan og Anakin leder en gruppe klonsoldater i eftersøgningen på hende. På sporet af hende kommer vores helte dybt ned i Karina den Stores skjulested. Til deres rædsel finder de ud af, at stedet vrimler med udøde forsvarere. Karina kan åbenbart vække de døde til live og tage kontrol over dem. Kan Obi-Wan og Anakin overkomme Karinas udøde horde og finde Luminara før det er for sent?

Ved fronten har de republikanske styrker desperat brug for medicinske forsyninger. Mens Jedi-ridderne transporterer Poggle the Lesser til Coruscant som fange, er de to Padawans Barriss Offee og Ahsoka Tano udsendt for at eskortere læge-fregatten til dens destination. Da geonosianske hjerneorme tager kontrol med klonsoldaterne ombord på deres forsyningsskib, må Ahsoka og Barriss kæmpe for at stoppe skibet fra at slippe den dødelige plage lås i galaksen.

Anakin, Obi-Wan og Ahsoka nødlander på Felucia og søger hjælp fra de lokale krydderibønder men finder ud af, at det faktisk er bønderne, som har brug for hjælp. På grund af Hondo Ohnaka og hans bande af pirater, som planlægger at stjæle deres afgrøder, har bønderne hyret fire dusørjægere til at beskytte deres værdier. I et ulige partnerskab må Jedi'erne arbejde sammen med bøndernes dusørjægere for at besejre Hondo og hans bande.

På Palpatines ordre transporterer republikken det frygtelige Zillo-monster tilbage til Coruscant for at undersøge det. Palpatine er ivrig efter at udtrække monsterets hemmeligheder og bruge dem militært, så han beordrer sine bedste videnskabsmænd til at undersøge og til sidst dråbe monsteret. Opfyldt af smerte og vrede slipper Zillo-monsteret ud fra laboratoriet og begynder at smadre byen. Snart finder Anakin, Padmé og Palpatine sig forfulgt af monsteret, mens Jedi'erne kæmper for at stoppe det. I et endeligt opgør står Jedi'erne overfor at redde millioner af uskyldiges liv i Coruscant ved at ødelægge Zillo-monsteret, som er det sidste af sin art.

Fast besluttet på at dræbe Jedi Master Mace Windu udgiver en ung Boba Fett sig som klonkadet og sniger sig ombord på en Jedi-krydser for at placerer en bombe i Windus kvarterer. Men Bobas plan går galt, da bomben ikke dræber Mace, og pludselig leder alle klonerne ombord efter sabotøren. Boba ødelægger skibers reaktor for at skabe en afledning, og snart begynder hele skibet at falde fra hinanden. Bobas nye kadet-kammerater reder ham, da de ikke er klar over, at han er synderen. Er Boba så besat af tanken om hævn, at han ikke vil gøre det samme for dem?

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.