When Anakin, Ahsoka and Obi-Wan crash on the lush rainforest planet of Felucia, they decide to help four bounty hunters protect local farmers from pirates intent on stealing their valuable crops. Obi-Wan and Anakin soon find out that the pirates are led by the duo's old foe, Hondo.

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 who runs off, leading Anakin and Ahsoka to raid and take over his ship.

With a magical amulet from Mother Talzin, Savage Opress lands on a junk planet in the Outer Rim and searches for his lost brother. With the help of the snake-like Morley, Savage finds his brother, the former Sith lord Darth Maul, who has been driven to insanity from his bisection and near-death experience on Naboo over ten years earlier.

Driven by hatred, Maul and Opress set out to take revenge on the Jedi who had sliced him in half. Maul sends a message to Obi-Wan Kenobi to confront him alone by murdering the inhabitants of a village on a distant planet. Upon arrival, Kenobi is attacked by both Maul and Opress, who leave the planet with Kenobi as their prisoner. Obi-Wan receives aid from an unlikely ally, Asajj Ventress, now a bounty hunter after the one million credit bounty on Opress. Outmatched, Obi-Wan and Ventress flee Maul and Savage in the ship's cockpit, leaving the two Dathomirian brothers to patiently stage their next move—with Maul vowing to exact his revenge on Obi-Wan.

R2-D2 is part of a team of Republic droids chosen for an important mission led by the diminutive Colonel Meebur Gascon to obtain an encryption module from a Separatist dreadnought. The droids must overcome numerous challenging obstacles to succeed in this crucial assignment.

After their ship crashes on a desolate planet, D-Squad and Colonel Gascon must find a way off to get back to Coruscant, or be stranded forever.

Colonel Gascon and D-Squad discover that Abafar, the planet they are trapped on, is Separatist-controlled, but they also discover a Republic Clone Commando named Gregor, who has been stranded on the planet as well. They must work together to get off the planet safely.

After believing themselves safe, Colonel Gascon and D-Squad discover that they are prisoners of the Separatists in a captured Republic cruiser, finding themselves enmeshed in thwarting a plot to destroy a Republic space station holding a strategic conference.

Maul proceeds to lure Obi-Wan Kenobi to Mandalore with news of Satine's capture. Obi-Wan infiltrates Mandalore, but ends up captured himself. Maul murders Satine, but Obi-Wan is rescued by Bo-Katan (who is revealed to be Satine's sister) and her Death Watch faction, who trigger a civil war against Maul. Meanwhile, the takeover captures the attention of Darth Sidious, Maul's former master, who travels to Mandalore to deal with the rogue Sith brothers. Seeing Maul as a rival, he duels Maul and Opress, which leads to Opress's death at the hands of Sidious. Maul, however, is spared, but only because Sidious has plans for him. The episode ends as Maul is continuously tortured by Sidious using force lightning.

Ahsoka and Bo-Katan contact Anakin Skywalker and Obi-Wan Kenobi, asking them for help in apprehending Darth Maul in his new hideout on Mandalore. While Obi-Wan is apprehensive, Anakin and the 501st give Ahsoka a warm welcome until news arrives that General Grievous and the Separatists are attacking Coruscant. Upon Anakin's suggestion, Rex (field-promoted to commander) and part of the 501st accompanies Ahsoka to Mandalore, forcing Maul's loyalists under Gar Saxon into retreat. Bo-Katan apprehends Prime Minister Almec, while Ahsoka follows a trail into the city's tunnel network, only to walk right into Maul's trap.

Ahsoka faces off against Maul, who mentions Darth Sidious before escaping. Ahsoka relays this to Obi-Wan, who says he had inferred from the recently killed Count Dooku that Sidious is the name of the Sith Lord who orchestrated the Clone Wars. Obi-Wan stresses that Maul must be taken alive as he may be their only chance to learn more about Darth Sidious. The captured Almec mentions that Maul had hoped to lure Anakin to Mandalore, but is assassinated by Saxon before he can reveal why. As Bo-Katan's and Rex's forces lead a final assault against Maul's Mandalorians, Ahsoka confronts Maul again, who reveals that Sidious has engineered the destruction of both the Republic and the Jedi and asks Ahsoka to join him to stop Sidious. When she demands to know his intentions with Anakin, Maul claims that Sidious wants to make him his new apprentice, and that he had hoped to kill Anakin before this happens. Refusing to believe him, Ahsoka fights Maul above the city, where she rescues him from falling to his death. She then leaves Maul to be captured by clone troopers, despite his frantic warnings that everyone will soon die.

With the Siege of Mandalore over, Ahsoka and Rex prepare to take Maul before the Jedi Council on Coruscant. Mace Windu and Yoda contact Ahsoka via hologram and reveal that Obi-Wan has tracked Grievous down to Utapau, indicating that the war may soon be over. On their way to Coruscant, however, Ahsoka senses Anakin falling to the dark side and helping Darth Sidious to kill Windu, moments before Sidious executes Order 66, which brands all Jedi as traitors to the Republic and orders their deaths. As Ahsoka's clone troopers, including Rex, suddenly turn on her, she is forced to escape. Rex resists the order just long enough to mention the incident with Fives, allowing Ahsoka to learn about the inhibitor chips. She releases Maul to create a distraction, then subdues and captures Rex. With the help of three astromech droids, Ahsoka removes the inhibitor chip from his brain, restoring his free will.

As Ahsoka and Rex try to escape from the cruiser, Maul destroys its hyperdrive, causing the vessel to drop out of hyperspace and into a nearby moon's gravitational field. Forced to fight their way through the clones, Ahsoka tries to prevent Maul from getting away in their shuttle but fails. Just barely clearing the doomed ship, Ahsoka and Rex escape to the moon, where they respectfully bury the clones and Ahsoka discards one of her lightsabers. Two years later, Anakin, now as Darth Vader, arrives on the moon and recovers Ahsoka's lightsaber from the wrecked cruiser.