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.

A peace conference between Separatists and Republic delegates is interrupted by Lux Bonteri, the son of a late Separatist Senator, who involves Ahsoka in his dangerous search to find justice for his mother's death.

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.

As the younglings return from Ilum with Ahsoka, their ship comes under attack by Hondo's gang of pirates. The children must use ingenious and improvised traps to thwart the brigands.

With Ahsoka captured by Hondo's pirates, the younglings work together to infiltrate the pirates' den, using their wits and courage to deceive Hondo Ohnaka and launch a daring rescue.

When General Grievous launches a full-scale attack on the pirate base on Florrum, Ahsoka and the younglings fight side-by-side with Hondo and his pirates to turn back the Separatist forces.

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.

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.