During the Clone Wars, Hunter was the leader of the Bad Batch, an elite group of clones called in for special missions for the Republic. On one occasion, he and his fellow troopers were sent to infiltrate a Separatist Cyber Center and learn valuable intel about the battle on Anaxes.

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.

After an disagreement during an Imperial mission to eliminate an insurgency of Separatist droids on Onderon, Hunter and Crosshair parted ways. While the rest of the Bad Batch defected from the new Empire alongside a child called Omega, who was a mutated clone like the rest of the Batch, Crosshair remained behind to serve the Empire.

Hunter quickly became a father figure to the young Omega. 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 in the changing galaxy. 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.

The child quickly proved to be a valuable asset to the team. On the Ordo Moon, Hunter was knocked unconscious while tracking a creature that had stolen a part from the ship, and Omega managed to finish the mission on her own.

But they couldn't hide from the Empire for long and on Pantora looking to secure supplies and make repairs to their ship, the bounty hunter Fennec Shand caught up to the crew and nearly captured Omega. Fortunately, Hunter gave chase and kept Omega safe.

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. In exchange, Cid helped to identify the bounty hunter that had tried to capture Omega.

The galaxy posed other dangers to the child's safety. On Corellia, Hunter worked with Trace and Rafa Martez to rescue Omega from being boiled alive in a droid decommissioning facility. 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.

However, even with their chips removed Crosshair and the Empire were on their trail. During a showdown on Bracca, Hunter and Omega evaded Crosshair only to be confronted by the bounty hunter Cad Bane. During the shoot-out, Hunter was blasted by the quick-draw's weapon and Omega was lost.

Hunter and his brothers were able to rescue Omega, 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 a watery grave, leaving Crosshair behind when he refused to join them once more.