As Ahsoka and her allies struggle to evade the Trandoshan hunters, their efforts receive an unexpected boost when a new captive arrives.

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.

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.

With freed prisoners in their possession and brutal warden Osi Sobeck 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.

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.

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.

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.

Obi-Wan, Anakin and Ahsoka become stranded on a mysterious planet where the Force is very strong. Three powerful entities called the Father, Son and Daughter live there. The Father tries to convince Anakin to stay and remain as Anakin will be the only one able to control the Son and Daughter since he is the Chosen One.

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. 

With the results of Ventress's attack on Dooku as a failure, Mother Talzin gives Dooku a new apprentice named Savage Opress, who is the clan brother of Darth Maul and secretly controlled by the Nightsisters.

Darth Sidious, troubled by Ventress's growing progress with the dark side of the Force, commands Count Dooku to eliminate her. When Ventress survives Dooku's assassination attempt, the jilted former apprentice vows to take revenge, enlisting her kinswomen – the Nightsisters of Dathomir – in her scheme.

Senators Padmé Amidala, Bail Organa and Onaconda Farr push against a new bill in the Senate to buy new clones for the Republic. But someone does not like their opposition and tries to persuade them out of it.

When the Senate begins debate on a bill that would eliminate government oversight of the Banking Clan's activities, Padmé and Ahsoka travel in secret to the capital of the Confederacy of Independent Systems, in an attempt to forge a peace agreement with the Separatists.

Due to his possession of incriminating information, Ziro the Hutt is placed under the custody under the Hutt Council. When Cad Bane is sent to hunt down Ziro, he learns that Jedi Masters Obi-Wan and Quinlan Vos are searching for Ziro too.

While on an important shopping trip on Coruscant, C-3PO and R2-D2 are kidnapped by the sinister bounty hunter Cad Bane in the dastardly plot to free Ziro the Hutt.

Having volunteered to protect Senator Padmé Amidala during a political mission to Alderaan, Padawan Ahsoka Tano is plagued by recurring visions of the presumed dead bounty hunter Aurra Sing assassinating the senator.

Ahsoka is assigned to teach a class at the cadet academy on Mandalore. Soon after she arrives, Duchess Satine's zealous nephew and his classmates uncover a nefarious plot.

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 facade.

Chairman Papanoida's family is kidnapped and held for ransom. Ahsoka must team 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.

With Ryloth under siege, a trapped Jedi Master Ima-Gun Di and his clone forces rally the local forces of Cham Syndulla. Elsewhere, the Jedi council sends Bail Organa and Jar Jar Binks to go to Toydaria, to ask King Katuunko for aid to Ryloth.

Note: This episode is a prequel to the Season One premiere, "Ambush" and the Ryloth Trilogy.

Taking place after the Season 1 episode "Rookies", General Grievous and Ventress's Separatists forces launch a major attack on the Republic cloning facilities on Kamino with Anakin, Obi-Wan, Jedi Master Shaak Ti, and the 501st defending it.

On Kamino, before the events of "Rookies" (Season 1 Episode 5), 5 clone cadets of Domino Squad are at risk of washing out unless they pull their team together while trainers Bric, El-Les, and Jedi Master Shaak Ti debate their fate.