To refrain from being thrown out of the Academy, five clone cadets must learn to work together and realise their future as soldiers of the Republic.
When the Separatists, led by Asajj Ventress and General Grievous, plan to destroy the cloning facilities on Kamino, Anakin and Obi-Wan come to aid the Clones in defending their home planet.
Jedi Master Di and Cham Syndulla's forces are trapped on Ryloth. Senator Bail Organa and Jar Jar Binks are sent to Toydaria to acquire help in saving the Jedi Master and local forces.
Chairman Papanodia's family is kidnapped and held for ransom. Ahsoka must team up with the Senator from Pantora, Riyo Chuchi, to aid the new chairman in recovering his family before the Trade Federation can unduly influence the future of his planet.
When Padme pays a visit to Duchess Satine on Mandalore, an epidemic hits the youth of one of the Academies. After some investigation, Satine and Padme uncover a conspiracy at play.
Much to her displeasure, Ahsoka is given the duty of teaching a class at the academy on Mandalore.
While on a mission to protect Senator Amidala, Ahsoka begins to have recurring visions of a certain bounty hunter.
Cad Bane captures C-3PO and interrogates him for information.
The hunt is on for Ziro the Hutt after he somehow manages to escape from his imprisonment.
Padme and Ahsoka travel behind enemy lines to attempt a peace treaty with the Confederacy of Independent Systems.
Senators Amidala, Organa, and Farr take the battefield to the Senate while trying to stop a bill that would create another batch of Clones to fight the never-ending war against the Separatists.
With the help of the Nightsisters of Dathomir, Asajj Ventress seeks revenge against her once Master, Count Dooku.