Fem egenrådige kloner kæmper med at færdiggøre deres træning på Kamino. Disse kadetter -- Hevy, Cutup, Droidbait, Fives og Echo -- er tilsyneladende et "dårligt kuld" og er ude af stand til at arbejde sammen som et hold. Mens Shaak Ti og eksercitsinstruktørerne Bric og El-Les diskuterer kadetternes skæbne, lærer klonerne at arbejde sammen og acceptere deres skæbne som soldater.

Republikken erfarer, at seperatisterne står overfor et angreb på Kamino, så Anakin og Obi-Wan haster til planeten. Efter republikken afværger seperatisternes afledningsangreb, begynder det egentlige angreb. Asajj Ventress, general Grievous og en hær af droider dukker op fra havene fast besluttet på at ødelægge Kaminos mulighed for at producere flere kloner. Rex, Cody, Fives og Echo leder klonerne i et desperat forsvar af deres hjemplanet.

Ryloth er under belejring. Fanget på overfladen samler Jedi Master Di de lokale styrker med hjælp fra Cham Syndulla. Desperate for at redde dem sender Jedi-rådet senator Bail Organa og repræsentant Jar Jar Binks til planeten Toydaria, hvor de skal overbevise den neutrale regent, kong Katuunko, til at sende hjælp til Ryloth. Bail og Jar Jar må overbevise Toydaria om, at det er det rette at gøre -- før det er for sent. Handelsføderationens udsending, Lott Dod, forsøger at få Toydaria til at forblive neutrale. Katuunko følger sin samvittighed og hjælper i hemmelighed republikken, hvilket Jar Jar formår at holde hemmeligt fra handelsføderationens nysgerrige agenter.

Formand Papanoidas døtre, Chi Eekway og Che Amanwe, bliver kidnappet og holdt for løsesum. Ahsoka Tano teamer op med senatoren fra Pantora, Riyo Chuchi, for at hjælpe formanden med at få sine døtre tilbage, før handelsføderationen kan nå at blande sig i hans planets fremtid. Formanden og hans søn, Ion, finder frem til kidnapperen -- Greedo -- på Tatooine og redder Che Amanwe. Imens finder Ahsoka og Chuchi ud af, at Chi Eekway bliver holdt fanget ombord på et af handelsføderationens blokadeskibe over Pantora, og de afslører skibets kaptajn Sib Canay som allieret med seperatisterne.

Mens Padmé er på en diplomatisk mission til Mandalore, garanterer hun den pacifistiske planet republikkens fulde beskyttelse, men hun og hertuginde Satine finder snart noget ondskabsfuldt under planetens ellers så rene overflade. Smuglere fra Moogan har sneget forsyninger ind, blandt andet te på flasker, som skulle have været leveret til Mandalores skoler. For at forøge deres indtægter, har de fortyndet teen med giftige kemikalier.

Ahsoka is assigned to teach a class at a leadership academy on Mandalore. Soon after she arrives, Duchess Satine's zealous nephew -- Korkie -- and his classmates uncover a nefarious plot. Prime Minister Almec is revealed to be an active part of the black market conspiracy on Mandalore, and he attempts to permanently silence Duchess Satine and the cadets before they expose his corruption. Ahsoka and the cadets defeat Almec before he can succeed.

In the middle of a routine shopping trip on Coruscant, C-3PO is abducted by the bounty hunter Cad Bane. Bane is looking for information about the Senate building on behalf of Jabba the Hutt. Finding C-3PO devoid of useful information, Bane and his accomplices kidnap R2-D2 and extract the vital data, before memory-wiping the droids of the incident, and letting them on their way. The floor-plans and security details of the Senate building are part of a plot engineered by the Hutt families to free their imprisoned brother, Ziro the Hutt, who holds potentially damaging information about Hutt activities.

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!

When the Senate begins debating a bill that would eliminate government oversight of the Banking Clan's activities in order to fund the war, Padmé and Ahsoka travel in secret to the capital of the Confederacy of Independent Systems. Amidala attempts to forge a peace agreement with the Separatists, while Ahsoka sees, for the first time, the people of the Confederacy. Padmé's friend, Mina Bonteri, spearheads the peace initiative, and convinces the Separatist Congress to sue for peace. Meanwhile, on Coruscant, Senators Lott Dod and Gume Saam conspire with Banking Clan representative Nix Card and Count Dooku to make the banking deregulation a reality. At Dooku's command, General Grievous engineers an attack at the central power distribution grid on Coruscant, carried out by Separatist demolition droids. The chaos and panic spreads to the Senate, which vehemently rejects the Separatist peace initiative.

Padmé, Bail Organa and Onaconda Farr attempt to rally Senators in opposition to a bill that would appropriate funds for millions of new clone troops and have disastrous financial consequences for the Republic. Their opposition to the measure, however, soon makes them targets for intimidation and attacks by hired guns. After escaping two hired thugs -- Chata Hyoki and Robonino -- in a harrowing speeder bike chase, Padmé is able to sway the Senate with a stirring account of how the war has affected an everyday civilian, her handmaiden Teckla Minnau.

Troubled by Asajj Ventress' growing prowess with the dark side of the Force, Darth Sidious commands Count Dooku to eliminate her. But Ventress survives Dooku's assassination attempt, and the jilted former apprentice vows to take revenge, enlisting the aid of her kinswomen -- the mystical Nightsisters -- in her sinister scheme. Mother Talzin, leader of the Nightsisters, veils Asajj and her fellow assassins in a cloak of invisibility, and they infiltrate Dooku's palace on Serenno. Though they fail to kill the Count, their use of captured Jedi lightsabers leads Dooku to mistakenly believe that the Jedi have tried to kill him. Interested in protection, he requests a new apprentice from Mother Talzin.

When Count Dooku calls upon the Nightsisters seeking a replacement for Ventress, she and her kin seize the opportunity to exact revenge. Ventress visits the far side of Dathomir and the males of the planet seeking the most brutal and powerful warrior among them. Talzin has Asajj secretly select a warrior from the distant Nightbrother village: Savage Opress. With the power of dark magic, Talzin transforms Savage into a hulking warrior ultimately loyal to Asajj. She then delivers Opress to Dooku, where he will serve as his secret Sith apprentice in a plot to overthrow Darth Sidious.

Anakin and Obi-Wan, sent to track down the mysterious figure behind the deaths of several Jedi, soon find themselves on the trail of the monstrous apprentice that Ventress has created: Savage Opress, who has been trained in the ways of the Sith by Dooku. When Opress returns to Count Dooku after an unsuccessful assignment, Ventress strikes. With Opress at her side, she attacks Dooku. Opress' loyalty is fleeting, however, and Dooku and Ventress discover that this new apprentice has a will of his own. When Savage returns to Mother Talzin, she gives him a new task: To seek the Outer Rim for his long-lost brother....

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.

Before the Jedi can leave Mortis, the Son takes Ahsoka captive in an attempt to entice Anakin into joining him to use their combined strength to overpower his Father and Sister. To this end, the Son casts Ahsoka under the spell of the dark side. Meanwhile, the Father attempts to stave off a disastrous showdown between his children and maintain the Force's increasingly precarious balance on the planet. Fearing that the Son may be unstoppable, the Daughter does the forbidden by taking Obi-Wan Kenobi to the Altar of Mortis, wherein is kept the Dagger of Mortis, a weapon capable of killing a Force-wielder. The Son steals the weapon, and attempts to use it against his Father to steal his power and end his rule, but the Daughter sacrifices herself, placing herself in front of the blade.

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.

With help from R2-D2 and a squad of captured battle droids, an elite team of Jedi and clone troopers led by Obi-Wan and Anakin attempt to free a captive Jedi general, Even Piell, from an impenetrable prison. Despite orders to the contrary, Ahsoka Tano tags along, though she proves indispensable when the infiltration mission begins to evolve. Piell and his fleet officer, Captain Tarkin, are liberated from their cells, but now the fugitives must escape the Citadel itself.

With freed prisoners in their possession and the brutal warden attempting desperately to thwart them, Obi-Wan and Anakin search for a way out of the Citadel and back to Coruscant. The prison, however, has more traps, perils and pitfalls in store for them than they had imagined and they must work past their differences if they are to escape. Their bid to board their shuttle fails when heavy weapons fire destroys the escape craft. Trooper Echo dies in the blast. The escapees then flee to the caves and call for rescue from the Jedi Temple on Coruscant.

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.

Ahsoka and a group of abducted younglings find themselves trapped on a Trandoshan moon, prey in an elaborate and cruel hunt. The forlorn younglings have lost all hope, despite the best efforts of their spirited leader, Kalifa. Ahsoka rallies them to defend themselves and strike back against the Trandoshan, an effort with deadly consequences.

As Ahsoka and her youngling allies struggle to evade the Trandoshan hunters, their efforts receive an unexpected boost when a new captive -- Chewbacca the Wookiee -- arrives. Chewie scrounges parts from a wrecked Trandoshan slave ship, assembling a communicator to send out a distress signal. Help arrives in the towering, shaggy form of Wookiee warriors led by General Tarfful. Freed from captivity, Ahsoka returns to the Jedi Temple and is reunited with Anakin Skywalker.