At the end of the first season, squad member "Crosshair" parted ways with the team due to differing beliefs. In the second season, several months have passed since the events on Kamino. Following the collapse of the Galactic Republic, the newly formed Galactic Empire has begun its brutal rule. Clone Force 99 (the Bad Batch), led by "Hunter," continues to fight for freedom. They reunite with their former comrade "Crosshair," encountering new friends and enemies along their perilous journey. As they struggle to find a way to survive in an ever-changing galaxy, characters such as Emperor Palpatine and the Wookiee Jedi Gungi also make appearances.