Shortly after the establishment of the Galactic Empire, the atypical clone commando team known as Clone Force 99 received orders for a mission on Onderon, tasking them with eliminating a supposed separatist base. The unit, however, discovered a community of refugees fleeing the Empire's rise, under the protection of Saw Gerrera and his Partisans, who had once fought for the Galactic Republic. Because the refugees included children, Clone Sergeant Hunter and the majority of his team refused to kill them. Crosshair, the team's sniper, demanded they follow orders, as his behavioral modification biochip had brainwashed him, making him the sole member aligned with the Empire. After meeting with Gerrera and allowing him, his fighters, and the civilians to leave, Hunter destroyed a probe droid sent by Admiral Wilhuff Tarkin to spy on them. Realizing they could not serve the Empire, Hunter chose to return to Kamino to rescue Omega, a young, enhanced clone who had tried to warn them about the mission.
Before their departure from Kamino, the effects of Crosshair's inhibitor chip were amplified, cementing his loyalty to the Empire and causing him to betray his former allies. Crosshair was subsequently dispatched on another assignment to Onderon, tasked with succeeding where Clone Force 99 had failed, accompanied by a unit of new Elite Squad Troopers, who were human recruits instead of clones. Crosshair's forces murdered all the refugees at the camp, but found that Gerrera was no longer present.
During the Clone Wars, the world of Onderon was embroiled in an internal conflict between the Separatist-aligned government, led by King Sanjay Rash, and a group of insurgents including siblings Saw and Steela Gerrera. The rebels eventually requested covert aid from the Jedi High Council, who dispatched Jedi Generals Anakin Skywalker and Obi-Wan Kenobi, Jedi Commander Ahsoka Tano, and Clone Captain Rex to provide supplies and training. The rebels ultimately succeeded in removing Rash and his Separatist supporters, restoring King Ramsis Dendup to power, but Steela was killed in the final battle. Saw, along with many other former rebels, continued fighting for the Galactic Republic, participating in the defense of Onderon when it was under siege near the end of the war.
In 19 BBY, the Clone Wars ended violently when Republic Supreme Chancellor Sheev Palpatine revealed himself as Darth Sidious, the Dark Lord of the Sith, and initiated Order 66, a secret directive compelling the clone troopers of the Grand Army of the Republic to betray and murder their Jedi commanders. This was enforced via inhibitor chips implanted in the clones' brains by the Kaminoan cloners at their creation, further brainwashing them into unquestioning obedience to Sidious. Soon after, Sidious' new Sith apprentice, Darth Vader, murdered the Executive Separatist Council and deactivated the Separatist Droid Army, ending the Confederacy of Independent Systems. Portraying the failed attempt by the Jedi to arrest him as an assassination attempt, Palpatine declared himself Emperor of the newly formed Galactic Empire. Gerrera immediately recognized the Empire's threat and refused to serve the new regime, as did many of his soldiers. Their refusal, coupled with the Empire's annexation of Onderon, forced them into hiding within Onderon's jungles along with civilian refugees under their protection, targeted for elimination by the Empire.
While most of the clone army succumbed to Order 66's brainwashing, a few clones remained unaffected, including most members of the unconventional clone commando squad Clone Force 99. The unit consisted almost entirely of genetically defective clones whose mutations granted them advantages in specific combat areas. In the cases of Clone Sergeant Hunter, Tech, and Wrecker, these mutations altered their brain activity, nullifying their chips. Echo, a later addition to the team, was an ARC trooper captured during the Battle of Lola Sayu and severely injured in an explosion. The Techno Union experimented on him, implanting extensive cybernetics before he was found alive and rescued, rendering his chip inoperable. However, Crosshair, the team's sniper, was an exception; while his altered brain activity affected his chip, it remained active, though less so than in standard clones. After Order 66, the other members of the "Bad Batch" noticed Crosshair's unusual behavior relatively quickly, starting with his attack on Jedi Commander Caleb Dume on Kaller, although Hunter allowed the Padawan to escape and falsely reported his death.
Shortly after the Empire's declaration, Admiral Wilhuff Tarkin visited Kamino to inform Prime Minister Lama Su of the Empire's intention to phase out clones and begin conscripting soldiers, supposedly due to cost concerns. Tarkin also planned to assess the clones' performance, deciding to observe Clone Force 99 after witnessing a cafeteria brawl between them and regular clone troopers. He was impressed by their performance in a combat evaluation he had switched to a live-fire exercise, but was concerned by their history of disobedience, although Lama Su and Chief Medical Scientist Nala Se argued it had never hindered their mission success. Tarkin, aware of Crosshair's secret report about Dume's escape, was skeptical about their true adherence to Order 66. He decided to test their loyalty by sending them to eliminate Gerrera and his people, deploying a probe droid to monitor the operation. However, Tarkin told the squad they were targeting a Separatist force, giving them the impression they were hunting remaining battle droids.
While stationed at Tipoca City after the Empire's proclamation, Hunter befriended Omega, a young female clone who worked as Nala Se's medical assistant and was fascinated by the Bad Batch. Her genetic enhancements made her highly perceptive, and she was present when Tarkin discussed the unit's loyalties with Lama Su and Nala Se. Sensing Tarkin's dislike of clones and suspecting his intentions, Omega approached Hunter before the squad's departure, urging him not to go. When he said he was going regardless, she asked him to take her with them, as Kamino was no longer safe. He refused, as she was not a soldier, and she warned him not to return to the planet afterward. Clone Force 99 departed Kamino in their shuttle, the Marauder.
The Marauder landed on Onderon two kilometers from Saw Gerrera's camp, and the Bad Batch proceeded on foot to the designated location. Hunter instructed Tech to scan for droids, but his scanners were being jammed. Upon reaching a vantage point overlooking the camp, Tech used his translation visor to survey the area, detecting heat signatures corresponding to people, not droids. Echo, using electrobinoculars, noted the presence of children, stating he was unsure if they were insurgents or Separatists. Surprised, Hunter took the binoculars to observe for himself. Wrecker asked if they would be fighting droids, and Tech clarified that there were none. Crosshair, noting Tarkin's instructions to target insurgents, aimed at an elderly woman in the camp and demanded Hunter authorize the attack.
Hunter realized they were surrounded by several of Gerrera's fighters. He ordered his squad to stand down to assess the situation. The rebels revealed themselves, and one suggested the clones comply with Hunter's request. Hunter lowered Wrecker's blaster and raised his hands, urging the others to surrender so they could hear the Onderonians' perspective. The Bad Batch were disarmed and escorted into the camp, where they saw the civilian refugees under Gerrera's protection. Echo noted the presence of former Republic fighters, and Tech questioned why they were sent to attack allies. Gerrera revealed himself, explaining they refused to fight for the Empire. Tech recognized Gerrera from reports about his history with Skywalker and Rex. One of the fighters took Hunter's blaster pistol and gave it to Gerrera.
The rebel leader surmised they were sent to wipe out his camp, and Hunter explained they were sent to eliminate insurgents. Gerrera sarcastically acknowledged his people's presence, asking if Hunter's group intended to eliminate them as the clones had the Jedi. Crosshair asked if that was a request, and Hunter snapped at him to stop. Gerrera ordered his people to pack up the camp and leave. Tech noted reports of the Jedi's attempt to kill Palpatine, but Gerrera suggested the massacre was to eliminate them, as Palpatine's control of the clone army and unjust self-coronation as Emperor would allow him to rule the galaxy unless stopped. Hunter noted Gerrera's lack of resources and manpower, but the rebel leader responded that unity could change things, suggesting a civil war was imminent.
As the group prepared to leave, one fighter asked Gerrera what to do with the clones. Gerrera noted the clones had once helped free Onderon, and turning to Hunter, offered them a choice: adapt to survive, or die with the past, returning Hunter's pistol. Gerrera, his fighters, and the civilians departed into the night, switching off the camp's central lamp. Wrecker retrieved the Batch's gear and handed Hunter his helmet before picking up the crate. The squad prepared to leave the clearing, but Hunter stopped, sensing something briefly. Crosshair also lingered before they left. Hunter had sensed a Viper probe droid sent by Tarkin, observing the entire encounter. The droid followed the Batch back to their starship.
As they returned to the Marauder, Tech remarked that with the Republic, they had always known where they stood, but not with the Empire. Crosshair insisted they complete the mission, and Echo told him to "wake up" as they were targeting innocent civilians. When Crosshair questioned their innocence, Hunter confronted him, demanding to know what was wrong. The sniper insisted he was following orders, which Hunter retorted was the problem. Crosshair argued the insurgents were plotting against the Emperor. As he and Hunter glared at each other, Hunter spotted the probe droid in the trees and shot it, realizing they were being followed. The squad inspected the remains, Wrecker expressing disbelief that Tarkin had spied on them. Echo noted the Jedi had never done that, although Crosshair suggested he simply hadn't known.
Hunter recalled Omega's words and realized the mission was a trap, adding she had warned him Kamino was unsafe. Wrecker agreed she might be right. When Crosshair questioned Hunter's trust in a child, Tech revealed he had deduced Omega was an enhanced clone with heightened perception. Echo questioned Tech's delay in mentioning it, the specialist's answer that he thought it was obvious being refuted by Wrecker. Hunter decided they owed Omega a rescue since she was one of them. Crosshair protested due to his brainwashing, but the others agreed. They boarded the Marauder and left Onderon.
Upon returning to Kamino, Tech noted Tipoca City's comscan was unusually silent. Landing the Marauder outside the hangar bays, the squad disembarked to find Omega and leave. However, they were ambushed by Coruscant Guard shock troopers and confronted by Tarkin, who accused them of treason for failing their mission. They were imprisoned in a brig, where they found Omega, locked up after the Coruscant Guard found her searching the Batch's barracks during the sweep. Hunter told her why they returned and asked her to leave with them, which she agreed to.
Tarkin, reviewing the probe droid's report, noted Crosshair's loyalty to the Empire and had him taken for examination, despite the Batch's protests. The examination revealed his inhibitor chip was partially functional, and Tarkin asked Nala Se if its effects could be enhanced to match standard clones. Crosshair underwent a painful procedure to boost his chip's effects. Now completely loyal to the Empire, Crosshair received new armor and weapons.
The remaining Bad Batch escaped imprisonment with Omega, heading to the hangar bay to reclaim their ship and equipment. Hunter intended to rescue Crosshair, but the brainwashed clone confronted his former squad in the hangar with several shock troopers, resulting in a tense firefight before the Bad Batch and Omega escaped in the Marauder.
As part of Project War-Mantle, which involved recruiting natural-born soldiers into the Imperial ranks, Tarkin and Vice Admiral Rampart placed Crosshair in command of a unit of four recruited Elite Squad Troopers. The group was sent on another assignment to Onderon to accomplish what the Bad Batch had refused, attacking a rebel camp and eliminating the fighters. At Crosshair's insistence, the recruits then murdered the refugees at the camp, although trooper ES-01 was executed for refusing. However, Gerrera was absent from the camp and avoided the massacre.