During the Clone Wars, Hunter was the leader of the Bad Batch, an elite group of clones including Wrecker, Tech, and Crosshair called in for special missions for the Republic. On Skako Minor, Clone Force 99 helped Anakin Skywalker and Clone Captain Rex get behind enemy lines to rescue the clone called Echo, who was previously thought lost in the escape from the Citadel. Echo later joined the Batch as its fifth member.

But at the end of the war, as the Emperor executed Order 66, Hunter and Crosshair came to blows. On Kaller, Hunter resisted the inhibitor chip and allowed the Padawan Caleb Dume to escape execution, while Crosshair insisted they follow their new orders to turn against the Jedi. Back on Kamino, Hunter and Clone Force 99 were tested by the Empire, which used live ammunition to assess their battle prowess in what was intended to be a training simulation.

While the rest of the Bad Batch defected from the new Empire alongside a child called Omega, Crosshair remained behind to serve the Empire. Hunter quickly became a father figure to the young Omega , who was a mutated clone like the rest of the Batch. Without orders to follow or a Republic to serve, Hunter's new mission was to keep the team together and find a way to survive. Initially, Hunter tried to send Omega to live with Cut Lawquane and his family, believing the former clone and his wife to be better guardians for a child. But Omega made it clear that she wanted to remain with Clone Force 99.

On Ord Mantell, Hunter brokered a deal with Cid, an old ally of the Jedi, creating work and a source of some income for his team that utilized their skills for the underworld.  They were always on the run, hunted by Imperials and bounty hunters like Cad Bane and Fennec Shand who saw Omega as a payday. But the reappearance of Clone Captain Rex forced Hunter to come to terms with the fact that the entire Bad Batch could be a threat to Omega if their inhibitor chips were activated.

After Omega was kidnapped, Hunter and his brothers were able to rescue her form Bane, but Hunter was captured by their former brother Crosshair. Ultimately, the mission to break Hunter out of Imperial lockup brought them all back to their homeworld of Kamino. Together, Hunter, Crosshair and the rest of Clone Force 99 witnessed the planet's destruction by the order of Vice Admiral Rampart and his Star Destroyers. The Bad Batch were presumed dead, but together they escaped, leaving Crosshair behind.

 Several months after the disaster on Kamino, Hunter and his team continued to work missions for Cid. They hunted for treasure at Dooku's castle on Serenno and took on a dangerous delivery of forged chain codes to the Vanguard Axis, as well as more mundane tasks like moving crates of nerf nuggets. One of their most desperate missions took Clone Force 99 to the Empire's stronghold, the former Republic capital of Coruscant. There, the Batch infiltrated Vice Admiral Rampart's docked Star Destroyer in search of valuable records that would prove it was the Empire that ordered the destruction of Kamino.

But that was far from the Empire’s only secret, as they would discover. The Batch was hunted by an elite assassin known as Clone X, and stumbled upon the Empire’s terrifying experimentation on the dangerous Zillo Beast. After being abandoned by Cid when their ship was stolen on Ipsidon, Hunter tried to find a home for his squad on the world of Pabu. For a brief moment, it was a peaceful existence where Omega could grow up with friends her own age. However, the Empire was still hunting Omega and holding Crosshair and other clones in captivity.

On a mission to Eriadu, Tech was killed trying to save the rest of the squad as they sought answers to the Empire’s scientific experimentation, and Hunter, Wrecker, and Omega were injured. Retreating to Ord Mantell to recuperate, Hunter was soon faced with an impossible choice: turn Omega over to the Empire or lose Wrecker, too. With help from Echo, Hunter and his last remaining squadmate escaped captivity, but Omega turned herself in to save her brothers. 

For months, Hunter and Wrecker scoured the galaxy for clues to Mount Tantiss, crossing the Pykes and working jobs for criminal elements like the Durand family in a desperate quest to gain intel to lead them back to their sister. A lead to Setron dead-ended in an abandoned Imperial medical facility, but they were able to rescue three young clone cadets who had been left behind. After reuniting with Omega on Ryloth’s moon, Hunter begrudgingly accepted Crosshair back into their lives. But the Empire was not about to give up on tracking Omega, sending their elite Clone X assassins to bombard Hunter and his squad on Teth after she was spotted among them. But with some help from Fennec Shand, he hoped to secure intel that might lead to Omega’s safety.