Before the end of the Clone Wars, while the Bad Batch - defective clones Hunter, Tech, Crosshair, and Wrecker plus cyborg clone Echo - are assisting Jedi Master Depa Billaba and her Padawan Caleb Dume on Kaller, Order 66 is issued and Billaba is killed by her clones. The Bad Batch receive the order too, but only Crosshair feels compelled to obey it, and Hunter lets Dume escape. Returning to Kamino, the Bad Batch learn that the war is over, that an Empire has replaced the Republic, and they meet a young girl, Omega, who is another defective clone. Admiral Tarkin arrives to evaluate the clones' viability, and sends the Bad Batch to eliminate a group of insurgents on Onderon. When they discover that these "insurgents" are actually fugitives under Saw Gerrera who refuse to submit to the new Empire, Hunter has his men abandon the mission and return for Omega. They are arrested for treason, and Tarkin has Crosshair's inhibitor chip enhanced, turning him against his squadmates and forcing the Bad Batch and Omega to flee without him.
Clone Force 99, the elite and experimental Clones of the Bad Batch, find their way in a rapidly changing galaxy in the immediate aftermath of the Clone Wars. Members of Bad Batch - a unique squad of clones who vary genetically from their brothers in the Clone Army - each possess a singular exceptional skill that makes them extraordinarily effective soldiers and a formidable crew.