Anakin and Ahsoka arrive at a pitched sky battle to help besieged Jedi General Aayla Secura. Anakin is gravely injured in the fight. Aayla and Ahsoka, along with the now-wounded Anakin, Rex, and the surviving clones, crash land on the uncharted grass-covered planet, Maridun. Forced to leave Anakin behind in order to save him, Aayla teaches Ahsoka why the Jedi have no personal attachments. They make their way to a Lurmen village. Their ruler, Tee Watt Kaa, explains that they're pacifists in this war and are not aligned with either side. Hesitant to have anything to do with the Jedi, Tee Watt Kaa agrees to help save Anakin's life.

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.

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.

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....

Count Dooku is determined to have revenge against the Nightsisters of Dathomir after their betrayal. General Grievous launches an all-out droid attack against the magic-wielding witches, and Mother Talzin and Asajj Ventress lead the defense with all the dark powers at their command.

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.

The dark warrior Savage Opress is on a quest to find his long-lost brother. Could Darth Maul truly be alive, after more than a decade since his gruesome bisection at the blade of Obi-Wan Kenobi? Savage voyages into the depths of a twisted planet to find whatever became of the fallen Sith Lord.

Savage and Maul, now reunited, pursue Obi-Wan Kenobi in search of revenge, and the Jedi Knight finds himself forced to unite with a surprising ally to defend against the deadly siblings.

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.