At the dawn of the Empire, Omega expressed an interest in joining the members of Clone Force 99, but the group's leader, Hunter, was initially unsure about allowing her among their ranks. After she warned them about the unscrupulous Admiral Tarkin ahead of a mission to Onderon, the Bad Batch returned to Kamino to save the young girl a mutated clone just like them. When Crosshair defected to the Empire, Omega alone showed compassion to the sharpshooter who seemingly could not control his impulses.

Caring for a child proved to be a challenge for the elite soldiers. On Saleucami, they tried to give Omega a chance at a normal life in the care of Cut Lawquane and his family. But Omega wanted to be with Clone Force 99, not left behind. On Pantora to refuel the Bad Batch's ship, the Marauder, and obtain needed supplies, Omega attracted the attention of the bounty hunter Fennec Shand. With help from Hunter, the girl evaded capture. When Omega attracted the attention of the bounty hunter Fennec Shand, Hunter helped keep her safe while Tech gifted her with Crosshair's old comm device so she could remain in communication with the rest of the squad should she become separated from them again.

The team soon settled in on Ord Mantell, finding work with a Trandoshan barkeep known as Cid. On a mission to Old Ord Mantell City, Omega found her own weapon, an energy bow, and proved an essential part of the team as they rescued a young rancor called Muchi. On another job, Omega made fast friends with Trace and Rafa Martez, as the two sisters fought the Batch for control of a Separatist tactical droid. With the former Republic clone army now fighting for the Empire, the Clone Wars-era droid had valuable information to defeat the soldiers.

Danger was around every corner, and sometimes in the places Omega least expected it. She knew from her training that the clones all had an inhibitor chip that forced them into submission to the Empire's orders against their will, and endangered anyone who defied the new regime. Still, it took the malfunction of Wrecker's inhibitor chip to force Clone Force 99 to take action and protect Omega from themselves. On Bracca, the Batch used discarded medical equipment to free themselves from the mind-controlling tech.

On a mission to Kamino that reunited Crosshair and the rest of Clone Force 99, the Bad Batch witnessed the planet's destruction by the order of Vice Admiral Rampart and his Star Destroyers. Hunter, Wrecker, Tech, Echo, and Omega were presumed dead, but together they escaped a watery grave, leaving Crosshair behind when he refused to join them.

Several months after the disaster on Kamino, Omega settled into life as a member of Clone Force 99. But she still had a lot to learn. On missions that took her and the team from treasure hunting in Dooku's castle on Serenno to acting as Cid's security detail at the riot racetrack of Safa Toma, Omega learned the value of loyalty and helping those in need, including getting the Jedi Gungi back to his homeworld of Kashyyyk. 

However, Omega could not escape her past. At the behest of Captain Rex, the Batch ventured into the heart of the Empire, seeking intel on Coruscant that would uncover Vice Admiral Rampart's lies about the destruction of Tipoca City. Dazzled by Senator Riyo Chuchi's poise and conviction, Omega began to see others like herself trying to help the citizens of the galaxy. But the mission also brought her face-to-face with Emperor Palpatine and a hard-won lesson: sometimes you can do the right thing in a situation and still lose. Even more heartbreaking, at the end of the mission Echo decided to leave Clone Force 99 to help Captain Rex and other clones in the galaxy.

Struggling with Echo’s loss, the remaining four members of the Batch continued to carve out a life for themselves with increasing difficulty. After their ship was stolen on a mission to Ipsidon, leaving them stranded with no help from Cid, they decided to cut ties with the Trandoshan. Retreating to a village on the tropical world of Pabu, Omega found a new community through Phee Genoa and her friends there. For a brief time, it was an idyllic life, filled with flying lessons from Tech and a new sense of belonging.

But the Empire was hunting Omega and her brothers. With new intel that Crosshair had been captured and imprisoned, the Batch traveled to Eriadu to track down Doctor Royce Hemlock, the chief scientist of the Advanced Science Division, in the hopes of following him back to his secret headquarters. However, during the mission, their covert infiltration was compromised and Omega and her brothers were trapped inside a railcar with no power. Tech was forced to execute Plan 99, sacrificing himself to save the others, a devastating loss for his sister.

Omega and her surviving brothers returned to Ord Mantell to nurse their physical and emotional wounds, walking into a trap. The Empire had found them. A ground assault brought Imperial commandos to their door, and Omega surrendered to Hemlock and his cronies as Hunter and Wrecker got away with help from Echo. Imprisoned on Mount Tantiss, Omega succeeded in locating Crosshair, but could do little to help her brother or herself. Instead, she returned to a life not unlike the one she had known on Kamino, assisting Nala Se working on secret medical experimentation, a prisoner of the Empire.

But Omega was not one to give up easily. Over her months of captivity, she fashioned a tooka from straw, befriended a lurca hound nicknamed Batcher, and tried to convince her brother, Crosshair, that escape was possible. After freeing the hound, Omega and Crosshair soon followed, escaping the secure facility with help from Nala Se’s datapad and a dire warning. After crash-landing on Lau in a stolen Imperial shuttle, Omega and Crosshair procured a second stolen vessel in a fire-fight with the Empire and succeeded in reuniting with Hunter and Wrecker on Ryloth’s moon. But although she was back safe among her brothers, the Empire already had a sample of her blood, and data that made her a high-value target for Dr. Hemlock.