Vijf koppige clone-cadetten, Hevy, Cutup, Droidbait, Fives en Echo, hebben moeite met het afronden van hun training op de oceaanplaneet van Kamino. Hoewel ze niet als team kunnen samenwerken, moeten ze leren hun toekomst als soldaten te omarmen, voordat ze van de academie worden gestuurd.

Als de Republiek ontdekt dat de Separatisten een aanval op Kamino voorbereiden, haasten Anakin Skywalker en Obi-Wan Kenobi zich om de planeet te beschermen.

Senator Bail Organa en afgevaardigde Jar Jar Binks worden naar de planeet Toydaria gestuurd, waar ze koning Katuunko moeten overtuigen om hulp te sturen naar Ryloth, voordat het te laat is.

Senator Padmé Amidala ontdekt een duistere samenzwering die op de loer ligt onder de rustige façade van Mandalore.

Tot haar ergernis wordt Ahsoka Tano aangewezen om een klas les te geven op de cadet-academie op Mandalore.

Ahsoka Tano wordt geplaagd door terugkerende visioenen van senator Padmé Amidala die doelwit wordt van een moordaanslag.

Tijdens een routine shopping-trip op Coruscant, worden C-3PO en R2-D2 ontvoerd door premiejager Cad Bane.

Nadat hij bevrijd is uit een gevangenis van de Republiek door premiejager Cad Bane, wordt Ziro the Hutt gezocht door de schimmige Hutt-raad.

Padmé Amidala en Ahsoka Tano reizen in het geheim naar Raxus in een poging een vredesakkoord te smeden met de Separatisten.

Senatoren Padmé Amidala, Bail Organa en Onaconda Farr worden doelwitten als ze een wetsvoorstel proberen tegen te houden dat miljoenen nieuwe clone-troepen zal creëren.

Geplaagd door Asajj Ventress' groeiende kundigheid binnen de Dark Side van de Force, beveelt Darth Sidious graaf Dooku haar te elimineren.

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.