Alarming rumors about the peace-abiding Duchess Satine of Mandalore prompt Obi-Wan to investigate the secluded planet. Satine wants to keep Mandalore neutral in the Clone Wars, but the actions of a violent splinter group -- Death Watch -- threaten to push the planet towards war.

A Separatist blockade surrounds Christophsis. Anakin's fleet is tasked with deploying relief supplies to the surface but they are massively out-gunned and out-maneuvered by the skillful Admiral Trench. Obi-Wan arrives and unveils the Republic's new weapon: a stealth ship. The stealth ship is the last hope at besting the cunning Separatist fleet commander and aiding the battered people of Christophsis.

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.

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.

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.

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.

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.

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.

After the Republic conquers an Umbaran airbase, General Krell orders Rex and his men on towards the heavily fortified capital. Realizing there's a better plan, several clone troopers disobey orders to carry out a rogue, covert operation.

With two of his men facing execution for disobeying orders, Captain Rex must confront his overly aggressive commander, General Krell. Risking charges of mutiny, Rex must make a dark choice as the true face of the enemy emerges.

Zygerrian slavers are behind the sudden disappearance of an entire colony of people on the planet Kiros. As Anakin and Ahsoka rush to defuse a series of bombs planted by the slavers, Obi-Wan must fight with their imposing leader.

When the Jedi learn of a Separatist plot to kidnap Chancellor Palpatine, one of them must go deep undercover as a hardened criminal to extract information from the conspirators.

An aimless Asajj Ventress joins a team of bounty hunters under the leadership of young Boba Fett. On an alien world, they undertake a dangerous but profitable mission that tests the limits of their skills, and the strength of Asajj's character.

After a rebel attempt to rescue Onderon's true king, Ramsis Dendup, an unexpected ally steps forward to halt Dendup's execution and aid the rebel cause.

Ahsoka escorts a group of younglings to Ilum, where they will learn from Yoda and undergo a crucial rite of passage: the construction of their lightsabers. They grapple with both physical and inner challenges as they face the dangerous task ahead of them.

After a comet damages their shuttle, R2-D2, Colonel Gascon, and the other droids crash on a desolate planet where they must make their way across a bewildering expanse of emptiness to carry out their mission.

Savage and Maul forge an alliance with Death Watch to target a common enemy: Obi-Wan Kenobi.

The fugitive Ahsoka escapes to the criminal depths of Coruscant.

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.

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.

The clones look to uncover the source of the Separatists' strategies...and bring in an elite squad called the Bad Batch.

After leaving the Jedi Order, Ahsoka Tano finds herself in the underworld of Coruscant where she befriends aspiring pilot Trace Martez. Enlisted by Trace’s sister Rafa to help build dangerous droids, Ahsoka opts to keep her Jedi past a secret.