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.

Padmé, on a diplomatic mission to Mandalore, guarantees the pacifist planet the Republic's full protection, but she and Duchess Satine soon find something sinister lurking beneath the planet's serene façade. Moogan smugglers have been sneaking in supplies, including bottled tea destined for the Mandalorian schools. To increase their profits, they have been diluting the tea with a hazardous chemical.