Five headstrong clones struggle to complete their training on Kamino. These cadets -- Hevy, Cutup, Droidbait, Fives and Echo -- seem to be a "bad batch" and are unable to work as a team. As Shaak Ti and drill instructors Bric and El-Les debate the cadets' fate, the clones learn to work together and accept their destiny as soldiers.

The Republic learns of an impending Separatist attack on Kamino, and Anakin and Obi-Wan hurry to the planet. After the Republic repulses the Separatists' diversionary assault, the real attack begins. Asajj Ventress, General Grievous and an army of droids rise out of the oceans, bent on destroying Kamino's clone production facilities. Rex, Cody, Fives, and Echo lead the clones in a desperate defense of their home planet.

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.