Clone trooper Tup is undergoing a medical examination in the sterile laboratories of Kamino to find the motives for his shocking attack on the Jedi master. For the examination to succeed, Arc Trooper Fives must enter the depth of Tup's mind, where he finds a secret code manipulation in the cloning program of the Republic.
The Grand Clone Army of the Republic, led by Jedi Masters Yoda, Mace Windu, Obi-Wan Kenobi and other Masters must fight the New Droid Army of the Separatists to defend the Republic and the political stability of the galaxy. They face the cunning Dooku, the vicious General Grievous and the relentless Asajj Ventress on the field of battle, all the while, behind the scenes, Senator Palpatine manipulates things to his benefit.
Meanwhile Jedi Knight Anakin Skywalker takes on a young Padawan apprentice named Ashoka Tano and is trying to train her to become a Jedi Knight in the midst of the Galactic War.