Five headstrong clones struggle to complete their training on Kamino. These cadets -- Hevy, Cutup, Droidbait, Fives and Echo -- seem to be a "bad batch" and are unable to work as a team. As Shaak Ti and drill instructors Bric and El-Les debate the cadets' fate, the clones learn to work together and accept their destiny as soldiers.

The Republic learns of an impending Separatist attack on Kamino, and Anakin and Obi-Wan hurry to the planet. After the Republic repulses the Separatists' diversionary assault, the real attack begins. Asajj Ventress, General Grievous and an army of droids rise out of the oceans, bent on destroying Kamino's clone production facilities. Rex, Cody, Fives, and Echo lead the clones in a desperate defense of their home planet.

Ryloth is under siege. Trapped on the surface, Jedi Master Di rallies the local forces with the help of Cham Syndulla. Desperate to save them, the Jedi Council dispatches Senator Bail Organa and Representative Jar Jar Binks to the planet Toydaria, where they are to convince the neutral regent, King Katuunko, to send aid to Ryloth. Bail and Jar Jar must convince Toydaria that their cause is just -- before it's too late. Trade Federation envoy Lott Dod attempts to prevent the Toydarians from giving up their neutrality. Katuunko follows his conscience and secretly aids the Republic, which Jar Jar is able to keep secret from the snooping Trade Federation agents with his inimitable distractions.

Chi Eekway and Che Amanwe, Chairman Papanoida's daughters, are kidnapped and held for ransom. Ahsoka Tano teams up with the Senator from Pantora, Riyo Chuchi, to aid the new chairman in recovering his family before the Trade Federation can unduly influence the future of his planet. The Chairman and his son, Ion, track down the kidnapper -- Greedo -- on Tatooine, and rescue Che Amanwe. Meanwhile, Ahsoka and Chuchi find Chi Eekway held captive aboard a blockading Trade Federation battleship over Pantora, and expose Trade Federation officer Sib Canay as a Separatist conspirator.

Padmé, on a diplomatic mission to Mandalore, guarantees the pacifist planet the Republic's full protection, but she and Duchess Satine soon find something sinister lurking beneath the planet's serene façade. Moogan smugglers have been sneaking in supplies, including bottled tea destined for the Mandalorian schools. To increase their profits, they have been diluting the tea with a hazardous chemical.

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.

Tasked to protect Senator Padmé Amidala during a political mission to Alderaan, Padawan Ahsoka Tano is plagued by recurring visions of recently-deceased bounty hunter, Aurra Sing. Unable to clear her mind, Ahsoka worries that the stress of conflict is finally getting to her until her visions indeed prove prophetic. Padmé narrowly avoids death when Aurra Sing attempts to assassinate her. Together, Padmé and Ahsoka trap the hunter, and Ahsoka discovers the true villain behind the plot to kill Padmé: the incarcerated gangster, Ziro the Hutt.

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.

Clone trooper Tup succumbs to a mysterious mental illness that results in the shocking death of a Jedi Master. Unable to account for his murderous actions, Tup is sedated and sent back to Kamino for examination. Meanwhile, Admiral Trench of the Separatists informs Count Dooku of the betrayal, and is convinced that the killing stems from something deeper. Anakin Skywalker and ARC Trooper Fives accompany Tup, but their return trip is ambushed by Separatists.

In the sterile laboratories of Kamino, the ailing clone trooper Tup and his friend ARC Trooper Fives are quarantined for examination following Tup's shocking murder of a Jedi Master. With the help of medical droid AZI-3, Fives is determined to get to the bottom of Tup's condition and uncovers a secret buried deep within the Republic's cloning program.

The body of clone trooper Tup is scheduled for transport to Coruscant, where Chancellor Palpatine's own doctors will closely examine it. ARC Trooper Fives breaks protocol and defies orders to dig up answers, and discovers that there is an organic construct of unknown purpose hidden in the brains of all clone troopers.

Fives continues to push for answers regarding the mystery of the clone contamination and secures an audience with Supreme Chancellor Palpatine. But the situation quickly collapses when Fives is accused of attacking the Chancellor, and he must flee deep into the Coruscant cityscape while pursued by fellow clone troopers.

While on Scipio to fund a mercy mission, Padmé Amidala is called upon by an old friend, Rush Clovis, to help uncover corruption in the Banking Clan. They must evade the bounty hunter Embo to escape the planet with the incriminating information.

Back on Coruscant, Clovis -- known traitor of the Republic -- makes a dubious deal which puts him at the head of the Banking Clan. Anakin's increasing distrust and hatred of Clovis strains his relationship with Padmé to the breaking point.

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.

Jar Jar Binks' beloved Queen Julia of the planet Bardotta has been abducted by the bloodthirsty Frangawl cult to fulfill a dark and ancient prophecy. Representative Binks and Jedi Master Windu must find the missing Queen before the cult can rise in power.

A Jedi mission finds a lightsaber belonging to the long-dead Master Sifo-Dyas, prompting Yoda, Obi-Wan Kenobi, and Anakin Skywalker to begin an investigation into his decade-old disappearance. This sparks Darth Sidious to order Darth Tyranus to clean up any loose ends that may lead the Jedi to discover the truth of the Sith conspiracy.

Yoda is deeply unsettled when he hears something from beyond the grave: the voice of Qui-Gon Jinn. Knowing that it is impossible for a Jedi to retain his identity after death, the Jedi Council begins to worry that Yoda may be corrupted by the influence of the dark side. Determined to find answers, Yoda escapes the Jedi Temple to follow the disembodied voice.

Letting the Force guide him, Yoda voyages into the heart of the galaxy to an ancient world that is one of the wellsprings of the Force and the source of midi-chlorians. Yoda undergoes difficult trials administered by the Five Priestesses, mysterious Force-wielders who hold the secret to immortality.

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.