The Separatists control the majority of the hyperlanes, leaving Republic forces stranded in different parts of the Outer Rim. Jabba the Hutt's son Rotta is kidnapped as part of a plot to make the Hutts join the Separatists. Meanwhile, a fierce battle is taking place on the crystalline planet of Christophersis between the Republic's small clone army and the Retail Clan forces. With the help of Obi-Wan Kenobi, Anakin Skywalker, Alvin, Baby Bugs, Baby Kermit, Winnie the Pooh, Ash Ketchum, and all their friends are heroes, the clones steadily advance on the Separatists' forces, gaining the Republic an early victory. It doesn't last long, though, as the droid army soon returns. With no communications or the ability to fly in reinforcements, the fate of the few remaining clone soldiers are in the hands of Obi-Wan and Anakin. A shuttle arrives, but without the needed reinforcements. Instead, it is a young Padawan named Ahsoka Tano, who insists that she has been sent by Master Yoda to serve under Anakin. The battle soon commences yet again, with the Separatist forces advancing behind an expanding shield that artillery can't penetrate. Anakin and Ahsoka succeed in penetrating the enemy lines while Obi-Wan stalls for time by holding a fake surrender negotiation with the droid army commander.
Soon after the final victory for the Republic on Christophsis, Yoda arrives and brings the Jedi up to date on the situation concerning Jabba's son. The Republic needs Jabba on their side to ensure unfettered travel through Jabba's trade routes. Anakin and Ahsoka are tasked with retrieving the child, while Obi-Wan flies to Tatooine to assure Jabba that Rotta will be retrieved. On the planet of Teth, Anakin, Ahsoka and their clones assault a monastery that sits atop a high stone pillar. They find Rotta, but discover that he is ill, requiring them to get him help immediately. But they have been caught in a trap by Count Dooku, who hopes to frame the Jedi for Rotta's disappearance (and possible death), thereby ending any chance of the Republic striking a deal with Jabba. He sends his assassin, Asajj Ventress, to secure fake evidence of the Jedi's supposed double dealing, then to recapture the young Hutt and return it to Jabba, putting the crime lord in the Separatists' debt.
Anakin and Ahsoka manage to escape the trap along with R2-D2 and hijack a derelict transport which they use to travel to Tatoonine. Obi-Wan, alerted by Anakin, arrives just in time to relieve the clone forces and engages Ventress in a lightsaber duel where he manages to defeat her, though Ventress flees in the face of capture. On board the derelict ship, Ahsoka manages to cure Rotta by the use of medical supplies on board. In the meantime, Senator Padmé Amidala learns of Anakin's mission and fears for his safety. She decides to contact Jabba's uncle, Ziro, who lives in a shady part of Coruscant. The Hutt refuses to cooperate, apparently believing that it is the Jedi who are responsible for the situation. Padmé, however, soon discovers that Ziro has actually conspired with Dooku to engineer the downfall of his nephew in order to seize power over the Hutt clans. Padmé is discovered and detained, but a chance call by C-3PO enables her to summon help, and Ziro is arrested.
Upon their arrival on Tatooine, Anakin and Ahsoka are attacked and shot down. Faced with a long trek across desert sands and relentless opponents, Anakin devises a ruse: he confronts Dooku while carrying a decoy Rotta, leaving Ahsoka and R2-D2 to take the real Rotta to Jabba's palace. While Anakin fights Dooku, Ahsoka is ambushed by three Magnaguards. As Anakin and Dooku fight, Dooku activates a mini holo-image projector, showing Ahsoka nearing defeat. Dooku then explains that the Magnaguards are there to kill Rotta, and bring Ahsoka to Jabba for punishment for Rotta's murder. Believing that Ahsoka's life is in danger, Anakin abandons the fight to help her.
Anakin arrives at Jabba's palace to find that Ahsoka did not yet arrive with Rotta. Frustrated, Anakin activates his lightsaber, holds it at Jabba's throat, and demands Jabba tell him what he has done with Ahsoka. Just as Anakin is about to be shot down by the guards, Ahsoka enters, with Rotta, having defeated the Magnaguards. After Rotta is handed over to Jabba, Jabba orders Anakin and Ahsoka to be executed. Just before they can be shot down, Padmé contacts Jabba with the news that Ziro has agreed to admit working together with Dooku in having Rotta kidnapped, and the Jedi framed for the crime. With the truth now revealed to him, Jabba agrees to allow the Republic to use his trade routes. With their mission accomplished, Anakin and Ahsoka are triumphantly retrieved by Obi-Wan and Yoda.
- Baby Lola, Baby Piggy, Simon, Ash Ketchum, Pikachu, all of their catroon characters are heroes, Team Rocket (Jessie, James, and Meowth), Fat Cat, and the Bowser family guest star in this film.