After he shoots the Jedi Master, Tiplar, during a combat, Clone Trooper Tup is interrogated by the Republic forces; However, he slips into a state of mental breakdown, after which Anakin and Rex see that Tup is best taken to Kamino to find out why his condition has deteriorated.
As Clone Trooper Tup and his friend, ARC Trooper Fives, are quarantined inside the Kamino to examine Tup and find out why he has killed the Jedi Master, Fives must get to the bottom of Tup's mind, only for him to discover a serious secret about the Republic's cloning program.
Tup's body is transported to Coruscant, where Chancellor Palpatine's doctors will examine it. After ARC Trooper Fives breaks the rules, he discovers that there is an ambiguous code planted inside the brains of all clone troopers.
As Fives pursues to look into the mystery behind Tup, he manages to schedule a private meeting with Supreme Chancellor Palpatine, but things soon turn upside down when Fives is falsely accused of attacking the Chancellor, only for him to flee and be chased by clone troopers.
Padmé's old friend, Rush Clovis, connects with her to ask for help while she is on a mission to the planet Scipio. For Clovis to eliminate corruption from the Banking Clan, he must see eye-to-eye with the bounty hunter, Embo, who tries to entrap them while they are running away from him.
To be in charge of the Banking Clan, Clovis contemplates a doubtful plan that will uncover corruption in Coruscant. Anakin's relationship with Padmé aggravates due to Anakin's ever-growing complications with Clovis.
As war breaks out in Scipio when the deal that Clovis has agreed on with the Separatists rebounds, the Republic's secessionist political leader, Count Dooku, intercedes, but only to the Republic's favor.
A dark prognostication jeopardizes the peaceful world of Bardotta, after which Queen Julia reaches out for her friend, the Senate Jar Jar Binks, to ask for his help, especially after some of the leaders have disappeared.
The Frangawl cult abducts Queen Julia due to the dark prognostication, after which Jedi Master Windu Mace is called to join Senate Jar Jar Binks for investigations and finding the kidnapped Queen.
Despite the fact that Master Sifo-Dyas has died in an ambiguous incident, a Jedi mission stumbles upon a lightsaber that belongs to him, only for Yoda, Obi-Wan, and Anakin to embark on their investigations to find out the reason behind his death.
As soon as Yoda is perturbed to hear the late Qui-Gon Jinn's voice coming out from where she is buried, he flees under the noses of the Jedi Council in an attempt to find Qui-Gon Jinn, especially that it is non-viable for a Jedi to rise from the dead.
It turns out that the Force is holding sway over Yoda and is controlling him, taking him to the heart of the galaxy, where he discovers the fountainhead of the Force and the midi-chlorians.
Yoda is called to Moraband, the home world of the Sith, where he comes face-to-face with the spirit of Darth Bane, who shows up with Count Dooku, and they both collude with one another against Yoda, who must struggle a bound to happen-clash that will lead him to preside over the galaxy.