The Clone Underground was a clandestine resistance movement. They stood against the newly established Galactic Empire and championed the cause of the defeated Galactic Republic. Their primary objective was to liberate and provide sanctuary for any clone troopers who had become disillusioned and desired to desert the Empire's ranks. Founded by former Clone Captain Rex in 19 BBY, the Clone Underground's base of operations was situated on the Wild Space planet of Teth. Rex and Echo, along with numerous other disaffected clones, launched attacks against the Empire alongside their allies. Their goals were to free imprisoned clones and to execute various anti-Imperial operations.
In 18 BBY, an Imperial clone X trooper discovered their base on Teth, leading to the near-total destruction of the Clone Underground in a subsequent attack by Imperial forces. Rex and a small group of survivors managed to escape the planet after appealing to Clone Commander Wolffe, who was leading the Imperial assault. Wolffe reluctantly granted them passage.
The Clone Underground was created by Rex as a resistance organization in 19 BBY, following the enactment of Order 66. The Clone Underground aimed to assist disillusioned clone troopers in escaping from the Imperial Military and to oppose the Empire in the name of the fallen Galactic Republic. By 18 BBY, the network had cultivated several clone contacts within the Empire who served as informants, including Slip until his demise. The group also had an ally within the Imperial Senate, a sympathetic senator named Riyo Chuchi. Throughout its existence, the network successfully rescued several clones, such as Gregor, Fireball, Nemec, Captain Howzer, and two additional clone troopers from his squad. Furthermore, Echo, a member of Clone Force 99 and a former Advanced Recon Commando, joined the network after the Imperial Defense Recruitment Bill was passed. Rex maintained communication with and occasionally received assistance from the other members of Clone Force 99, namely Hunter, Omega, Wrecker, Tech, and Crosshair.
The network utilized a ship called the Remora, which was equipped with a detachable leech vessel, as well as several captured Rho-class transport shuttles. The Clone Underground was dedicated to rescuing clone troopers, upholding their fraternal bonds, and carrying out actions that disrupted the growth of the nascent Galactic Empire. The network's secret base was located on the Wild Space planet of Teth, within the ruins of a deserted B'omarr Order Monastery. They also made use of a repair shop on Coruscant.
The Clone Underground was composed of numerous clone soldiers. Former Clone Commander Rex served as the leader of the organization. Other clone officers included clone commando Captain Gregor, CT-99 clone commando Corporal Echo and Captain Howzer. The Clone Underground also consisted of troopers such as Fireball, Greer, Nemec, Samson, a clone who wore armor with orange markings, and another clone who wore armor with red markings. Rex and the Clone Underground briefly collaborated with the Imperial trooper Slip and, on occasion, worked with the genetically modified Clone Force 99. Following her defection from the Empire, Emerie Karr, a former Chief Scientist, agreed to join the Clone Underground, desiring to atone for her previous actions, along with former clone prisoner Vik and many other clones that were imprisoned in the Galactic Empire's Tantiss Base.
Echo, Gregor, Nemec, and Fireball piloted the Remora to attack an Imperial Gozanti-class cruiser commanded by Captain Pearce above the planet Balmorra. The Remora successfully disabled the cruiser's hyperdrive and defensive systems. Echo and Nemec then led a boarding party that breached the cruiser's upper hull as Gregor docked with the Imperial vessel. They stormed the ship, liberated the prisoners, and attacked the bridge. While Echo attempted to extract data from the databank, Nemec interrogated Captain Pearce, who committed suicide by activating a suicide shocker implanted in his mouth. Gregor informed Echo and Nemec that they had freed the prisoners and ordered them to retreat due to the arrival of Imperial reinforcements. They boarded the Remora and jumped to hyperspace.
The clones then traveled to Trace Martez's repair shop on Coruscant, where Senator Riyo Chuchi met with the rescued three clones, including Howzer. Chuchi listened intently as Howzer recounted what he remembered from the prison to her and Echo.
Later, Rex, Howzer, Nemec, Samson, and Greer journeyed to Pantora to safeguard the fugitive Senator Avi Singh and his RA-7 protocol droid GS-8. Rex guided them towards a clandestine meeting with Senator Chuchi. Howzer maintained watch from a balcony, communicating with Samson and Greer, who provided security inside the building. Nemec guarded the two senators alongside Rex. Singh and Chuchi discussed the increasing opposition to Emperor Palpatine when a Clone X trooper CX-1 launched an attack, secretly killing Greer before throwing a bomb at the senators. Rex seized the bomb and threw it out of the room, causing an explosion that created a hole in the wall. Rex and Nemec then pursued CX-1 underground and up a tower, where Howzer arrived on a speeder bike and stunned the attacker. The clones then traveled on a shuttle through hyperspace with CX-1. Rex and Howzer discussed the object they had recovered from their prisoner, a data puck. Rex instructed Howzer to arrange for Fireball to examine the object at their base camp, the B'omarr Order Monastery on Teth.
Following the capture of the assassin, the Clone Underground brought him back to the B'Omarr Order Monastery to be interrogated. However, the clone proved resistant to interrogation, frustrating the Underground members who considered him their only lead to the location of Tantiss Base. Growing increasingly desperate, Howzer argued that they needed to contact Clone Force 99, a unit of clone commandos who had retired to the planet Pabu. He reasoned that one of their members, Crosshair, was also imprisoned at the Base and that Howzer suspected Crosshair knew the location due to his previous Imperial affiliation. However, another assassin was deployed to Teth on a mission to eliminate CX-1. He infiltrated the monastery and called for a Recovery Strike Team to reinforce him after identifying the presence of Omega in the compound. In the resulting firefight, the assassin killed many clones, including Fireball, Nemec, Samson, along with a clone who used armor with orange markings, and another clone who used armor with red markings, and forced the remaining clones (Rex, Howzer, and Clone Force 99) to flee into the jungle, where they were cornered by the Strike Team. Rex, recognizing Wolffe, pleaded with him to recognize the harm of his actions. Despite hesitating, Wolffe ordered his troopers to stand down and allowed the clones to board the Remora, which Echo and Gregor had just landed behind them, as a sign of respect to his clone brothers.