During the Onderon insurgency, a mission to Onderon occurred shortly after the formation of the Galactic Empire. During the mission, Clone Commander CT-9904 "Crosshair" and a team of newly conscripted recruits attacked a group of Saw Gerrera's rebels on Onderon, which resulted in the forces being wiped out.
In 19 BBY, the Clone Wars between the Galactic Republic and the Confederacy of Independent Systems came to an end through unexpected violence: the Dark Lord of the Sith Darth Sidious, who had masterminded the entire conflict, issued Order 66 to the clone troopers of the Grand Army of the Republic, which forced them to turn on and execute their Jedi commanding officers by activating secret behavioral modification biochips implanted inside them by the Kaminoan cloners. With the shutdown of the Separatist Droid Army shortly thereafter by Sidious' Sith apprentice Darth Vader, Sidious, in his public identity as the Republic's Supreme Chancellor Sheev Palpatine, declared the war over and a nonexistent "Jedi rebellion" crushed, before reorganizing the Republic into the Galactic Empire.
Although almost all of the clones had been brainwashed into mindless obedience to Sidious and his Empire, there were a few exceptions, among them most of the members of Clone Force 99, an irregular clone commando unit composed largely of genetically defective clones whose enhancements protected them from their chips. Participating in a battle on Kaller at the moment Order 66 was issued, the squad watched in horror and confusion as Jedi General Depa Billaba was executed by her own soldiers, before her Padawan Caleb Dume fled. Clone Sergeant Hunter followed Dume in an attempt to help him, but as backup he brought his team's sniper, CT-9904 "Crosshair", who was the only member of the so-called "Bad Batch" to be affected by the command. Crosshair thus attacked Dume, who managed to briefly knock him out before escaping from both clones. Hunter claimed to Crosshair that Dume had fallen to his death in a ravine after being stunned, but Crosshair realized he was lying.
After the Bad Batch returned to Kamino, Crosshair secretly filed a report of Dume's survival. Shortly after the declaration of the Empire, Admiral and Governor Wilhuff Tarkin visited Kamino to inspect the clones and inform the Kaminoans that the Empire did not intend to continue purchasing clones. As part of his evaluations, Tarkin had Clone Force 99 undergo a combat evaluation where their skills and ingenious tactics impressed him, but he was concerned about their tendency for disobedience, specifically noting Crosshair's report and that it could not be certain whether they had executed Order 66. Tarkin decided to test the squad's loyalty by sending them on a mission to Onderon to wipe out a group of former Republic fighters led by Saw Gerrera, a former leader of rebels against a Separatist-backed king during the planet's civil war. Gerrera, who had continued to fight for the Republic after the civil war ended, had refused to serve the Empire, forcing him, his fighters, and civilian refugees under their protection into hiding in Onderon's jungle.
The team is surprised to find the insurgents are mostly just refugees.
Having been told they were going after Separatist insurgents, the Bad Batch was surprised to discover the true nature of their targets, and all of them, except for the brainwashed Crosshair, refused to carry out the mission. After speaking with Gerrera, Hunter let him and his people leave peacefully, before discovering that Tarkin had been spying on them with a probe droid. Most of the Batch decided they were done serving the Empire, but Hunter decided to return to Kamino to rescue Omega, a young enhanced clone the squad had recently met who had attempted to warn him about going on the mission. On their return to Tipoca City, the Bad Batch was arrested and thrown in the brig, where they found Omega, who had been locked up by the Coruscant Guard after they found her in the squad's barracks.
From the probe droid's report, Tarkin learned that Crosshair had expressed loyalty to the Empire on Onderon, and had him taken away by Imperial shock troopers. A medical examination performed by Doctor Nala Se revealed that the sniper's inhibitor chip was active, but less so than in the standard clones. At Tarkin's request, Crosshair was subjected to a procedure where the chip's effects were amplified, making him totally loyal to the Empire. The remaining Bad Batch and Omega escaped from their cell and located their starship and equipment, hoping to find and rescue Crosshair, but the mind-controlled sniper confronted them in a hangar with a squad of shock troopers. After a tense firefight, the Bad Batch and Omega fled Kamino in the Marauder.
As part of Project War-Mantle, the Empire's plan to recruit natural-born soldiers, Vice Admiral Edmon Rampart had selected four skilled soldiers from across the galaxy to be the first Elite Squad Troopers. Under Tarkin's supervision, the new unit was placed under the command of Crosshair, who had been given the rank of Clone Commander, as part of their training. Tarkin had the unit sent to Onderon to do what Clone Force 99 had failed to do and kill Gerrera, and they were dispatched in a Nu-class shuttle. ES-01, one of the recruits, looked down on Crosshair for being a clone and aspired to take over command of the unit himself, making no secret of his ambitions.
The squad landed on Onderon near a rebel camp where several of Gerrera's fighters were preparing to pack up and leave, intending to transport several refugees under their protection to a rendezvous elsewhere in an LAAT/le patrol gunship. Gerrera himself, however, was not at the camp. The first sign the rebel commander had of an approaching enemy was when sensors were tripped in Sector 2A. The attack began immediately afterwards, as Crosshair shot several of the rebel fighters from a position within the trees before signaling his troops to move in.
The squad eliminates the rebels on Onderon.
The rebels fired back as they moved the refugees inside the gunship, but could not locate the enemy as they continued to take casualties. The Imperial troopers used both blasters and a flamethrower to press the rebels. One rebel's missile launcher was set off after its wielder's death, sending a rocket into nearby ruins. The rebel commander attempted to take control of the gunship after the survivors were onboard, but he was shot through the viewport by an Elite Squad Trooper who had flanked the camp and taken up a position in a tree.
The refugees and one surviving rebel were forced out of the gunship. As the rebel raised her hands, Crosshair interrogated her as to Gerrera's whereabouts. She replied that she did not know and would not say even if she did, whereupon she was executed. Crosshair then prepared to execute the civilians, which shocked the recruits. ES-01 loudly protested, saying that he and the others had not signed up to join an execution squad. Attempting to take over, he said that none of the recruits would follow the order and attempted to get the others to ignore the clone and commence taking the refugees into custody. Crosshair confronted him, explaining that the reason he had been placed in command was because he would follow orders, before executing ES-01 for disobedience. He then ordered the other recruits to carry out the execution, which they did.
The squad reports their success to Moff Tarkin and Admiral Rampart.
The remaining Elite Squad returned to Kamino, where Crosshair reported that Gerrera had not been at the camp, but everyone else had been neutralized. Tarkin noted that the unit had lost a soldier, but Rampart argued while it was unfortunate, casualties occurred in war. Pleased with how the project was shaping up and how Crosshair's new team had succeeded where his brothers had failed, Tarkin had left the project under Rampart's full supervision but warned his colleague that the Empire wasn't ready to abandon the clone army until they had enough recruits to have the Emperor retire the Old Republic soldiers.
The barracks in Tipoca City formerly used by the Bad Batch were reassigned to the Elite Squad, and after the unit arrived there, Crosshair reclaimed his former bunk, but was left pensive by the room's remaining traces of its former occupants.
Kaminoan Prime Minister Lama Su and Nala Se were both highly concerned by the Empire's plans for recruitment. Hoping to ensure continued business from the Empire, Lama Su authorized Nala Se to continue working on an experiment for a superior kind of clone. However, the clones they required genetic samples from would not return to Kamino willingly. Considering them Kaminoan property, Lama Su thought that they would only require one of the clones for their project to succeed.
- Star Wars: Timelines