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.

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.

Jar Jar Binks' beloved Queen Julia of the planet Bardotta has been abducted by the bloodthirsty Frangawl cult to fulfill a dark and ancient prophecy. Representative Binks and Jedi Master Windu must find the missing Queen before the cult can rise in power.

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.