A conflict unfolded at the B'omarr Order Monastery located on the planetary body Teth circa 18 BBY. This occurred when a soldier from the Clone X trooper unit uncovered the clandestine headquarters of the Clone Underground at that location. The clone trooper, who was in pursuit of a comrade captured by the Underground, infiltrated the religious site. After confirming genetically defective clone Omega's presence, he requested support from a Recovery Strike Team. During the subsequent exchange of fire, the assassin eliminated numerous insurgents, forcing the remaining clones to retreat into the woodland, where the Strike Team trapped them. Although Captain Wolffe permitted the clones to escape, the engagement led to the Clone Underground's disintegration and the destruction of their main base.
The Clone Underground represented a clandestine resistance movement established by Clone Captain Rex and former Advanced Reconnaissance Commando Echo, with assistance from Imperial Senators Riyo Chuchi and Avi Singh. Operating from a mechanic shop on the Imperial homeworld planet Coruscant, their objective was to aid the remaining clone soldiers who were either discarded or mistreated by the Empire following the Clone Wars. Upon learning of Tantiss Base, the headquarters of the Advanced Science Division where experiments were being conducted on hundreds of imprisoned clones, the Underground shifted its focus to locating the base to attack it and free their comrades. To achieve this, they established a base on the Wild Space planet Teth, within the B'omarr Order Monastery, the site of the Battle of Teth, and began recruiting more troopers to prepare for the eventual assault.
Around 18 BBY, Underground operatives Rex, Howzer, and Greer escorted dissenting Senator Avi Singh to Pantora, where he convened with Underground member Senator Chuchi to discuss a political alliance against Galactic Emperor Sheev Palpatine. Despite their precautions, a clone assassin from the Clone X trooper division discovered the meeting, incapacitating Greer and infiltrating the tavern where the discussion was taking place. When Greer failed to respond to communication device checks, Howzer and Rex investigated his location and found the assassin. He attempted to flee, but Howzer incapacitated him. The Underground members apprehended the assassin and transported him back to the Monastery on the Remora for interrogation.
After securing the prisoner, identified as CX-1 at the base, Fireball successfully disarmed his self-destruct device before the assassin could use it. However, the clone proved resistant to questioning, frustrating the Underground members who saw him as their only means of discovering Tantiss Base's location. Growing increasingly desperate, Howzer argued that they needed to contact Clone Force 99, a unit of genetically modified clones retired to the planet Pabu, as one of their members, Crosshair, was also imprisoned at the Base. Howzer suspected Crosshair knew its location due to his previous affiliation with the Empire.
Meanwhile, clone commando Scorch, the head of security at Tantiss Base, noticed that CX-1 had ceased responding to communication signals after his mission on Pantora. Since the assassin's implanted tracking device was still active, Scorch concluded that he had been captured. He activated another Clone X trooper, CX-2, to locate and silence him before he could reveal sensitive information. CX-2 tracked CX-1 to the monastery on Teth, arriving shortly after Clone Force 99.
While the Underground members were having lunch with Force 99, the assassin scaled the Monastery's spire and breached the compound's walls. Avoiding the guards, he planted two explosive devices on the Rho-class transport ships parked in the courtyard and entered the temple undetected. Before reaching his target, he spotted Omega, identified as a primary target by Advanced Science Division director Royce Hemlock, and quickly retreated to the courtyard to alert Scorch. The commando immediately dispatched a Recovery Strike Team under Clone Captain Wolffe and commando Hilo to reinforce CX-2, instructing the assassin to capture Omega alive.
Upon receiving his orders, CX-2 entered the temple and proceeded to the break room before detonating the explosives, resulting in the deaths of Samson and two other Underground clones. As the remaining rogue clones were interrogating CX-1, they were trapped in his small cell and unable to escape when the explosions occurred. CX-2 immediately eliminated CX-1 with a long range weapon and engaged the rogue clones, who managed to temporarily subdue him as Nemec was activating the backup energy source to send a distress signal to off-world Underground members. CX-2 destroyed the generator, injuring Nemec, and forcing the remaining clones to attack him, with Fireball using a portable incinerator against him. Unfortunately, CX-2 shot and killed Fireball, who dropped his flamethrower. The flames ignited the remaining explosives, detonating and collapsing part of the roof. As the cave-in trapped CX-2, the clones escaped through a tunnel in CX-1's cell, heading towards a small craft several levels underground.
Shortly after the shootout, the Strike Team's Rho-class shuttles landed in the Monastery courtyard, deploying the recovery unit led by Captain Wolffe. CX-2 briefed the officer, who reprimanded him for using explosives to pursue a target who was to be captured alive, emphasizing that the assassin was to follow his orders from that point forward. Wolffe then deployed a unit to search the ruins for escape routes, discovering the tunnel in the cell's floor and CX-1's body. Recognizing the Battle of Teth's history, Wolffe determined that the tunnel led to the Monastery spire's center and ordered the shuttles to split up. One descended to a platform at the spire's base, while the other circled the geologic feature to search for signs of escape vehicle. Wolffe also instructed a TK stormtrooper to destroy the cell to seal the tunnel entrance, forcing the escapees to confront them directly. Before the explosives detonated, CX-2 jumped into the tunnel to pursue the clones.
Inside the tunnel, the clones descended a staircase towards the leech vessel launch point. Before reaching it, CX-2 engaged them from several levels above, forcing Crosshair to stay behind to fight him while the others continued. After Crosshair fired an explosive bolt at the enemy, knocking him down several levels, the rogue clones reached the vessel before their pursuers and escaped to a predetermined extraction point in the jungle. However, before they could land, CX-2 reached the launch tube and shot their propulsion system, causing the shuttle to crash after transmitting an emergency message to off-world Underground members. The Strike Team arrived at the tube room, and Wolffe again reprimanded the assassin for disobeying his orders and shooting to kill instead of incapacitating, with CX-2 arguing that he only prevented the rogues from escaping. Tracking their transmissions, Wolffe ordered one of the two shuttles to fly ahead to their destination and block it off, while the rest of the Strike Team boarded the second one and pursued.
With the rogue clones' craft destroyed, the team made their way to the extraction zone's clearing. CX-2 soon caught up and engaged them with his rifle, but the clones evaded him until they reached the blockade formed by the TK stormtroopers from the Rho-class shuttle. With the shuttle hovering above, the clones deployed obscurants and attacked the stormtroopers through the smokescreen, killing several of them. Crosshair then shot the shuttle's pilot and its engines as more stormtroopers prepared to rappel from it, causing it to crash nearby.
CX-2, still in pursuit, engaged them again from a vantage point on a nearby hill. As the team ran for the extraction zone at the base of a cascade, Crosshair stayed behind and engaged the assassin in a sniping duel. The rogue clone disarmed his opponent, who switched to his sidearm and then a combat knife, before resorting to hand-to-hand combat. The two clones fell into the waterfall, where Howzer incapacitated the assassin, causing him to fall down the cliff.
The clones regrouped at the waterfall, awaiting their extraction craft. The second shuttle carrying Wolffe and commando Hilo arrived, and the Strike Team disembarked, surrounding the rogues with their backs to the waterfall cliff. Rex, recognizing Wolffe from their time in the Clone Wars, pleaded with him to recognize the harm of his actions, highlighting his pursuit of Omega—a child—as an example of Imperial indoctrination. Despite hesitating, Wolffe ordered his troopers to stand down and allowed the clones to board the Remora, which had just landed behind them, as a sign of respect for his clone brothers.