The Clone Underground was an underground resistance network of rebellious clone troopers that fought against the newly formed Galactic Empire, with their main goal being to free and shelter any disillusioned clones that wished to defect from its ranks. Established by former Clone Captain Rex in 19 BBY, the Clone Underground operated out of the Wild Space planet of Teth. Joined by other disillusioned clones, Rex and his companions began striking against the Empire to free imprisoned clones and conduct other anti-Imperial operations.
In 19 BBY, following the execution of Order 66, the Clone Underground was established by Rex as a resistance network. The goals of the Clone Underground included helping clone troopers escape the Imperial Military and fighting the Empire in the name of the fallen Galactic Republic. By 18 BBY, the network had several clone contacts within the Empire working as informants, such as Slip until his death. The group also had a sympathetic senator in the Imperial Senate itself, Riyo Chuchi. The network managed to rescue multiple clones throughout its history, including Gregor, Fireball, Nemec, Captain Howzer, and two other clone troopers from his squad. Additionally, Clone Force 99 member and former Advanced Recon Commando, Echo, joined the network following the passing of the Imperial Defense Recruitment Bill. Rex maintained contact with and was occasionally assisted by the rest of Clone Force 99, which included Hunter, Omega, Wrecker, Tech, and Crosshair.
The network possessed a ship known as the Remora that was equipped with a detachable leech vessel, as well as several Rho-class transport shuttles. The Clone Underground helped rescue clone troopers as per their bond as brothers and conducted other actions that harried the spread of the fledgling Galactic Empire. The network's hideout was on the Wild Space planet of Teth within the ruins of an abandoned B'omarr Order Monastery, though they also made use of a repair shop on Coruscant.
The Clone Underground movement consisted of multiple clone members. Within the movement's ranks were former Clone Commander Rex, who served as the leader of the organization. Other clone officers included clone commando Captain Gregor, Corporal Echo and Captain Howzer. Troopers within the Clone Underground included Fireball, Greer, Nemec, Samson, a clone who used armor with orange markings, and another clone who used armor with red markings. Rex and the Clone Underground were connected with the trooper Slip, and at times operated with the rogue clone commando Clone Force 99 unit. Following her desertion of the Empire, former Chief Scientist Emerie Karr agreed to join the Clone Underground, eager to make up for her past misdeeds.
Echo, Gregor, Nemec, and Fireball flew the Remora to attack an Imperial Gozanti-class cruiser under the command of Captain Pearce over the planet Balmorra. The Remora disabled the cruiser's hyperdrive and defenses. Echo and Nemec then led a boarding party that drilled through the upper hull of the cruiser as Gregor docked with the Imperial cruiser. Storming the ship, they freed the prisoners and attacked the bridge. While Echo attempted to retrieve 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 liberated the prisoners and to retreat as Imperial reinforcements arrived. They boarded the Remora and fled to hyperspace.
The clones then went to Trace Martez's repair shop on Coruscant, where Senator Riyo Chuchi met with the rescued three clones, including Howzer. A concerned Chuchi listened to Howzer tell her and Echo what he remembered from the prison.
Later, Rex, Howzer, Nemec, Samson, and Greer traveled to Pantora to protect the fugitive Senator Avi Singh and his RA-7 protocol droid GS-8. Rex guided them towards a secret meeting with Senator Chuchi as Howzer kept watch from a balcony, corresponding with Samson and Greer who was security on the inside of the building, with Nemec guarding the two senators along with Rex. Singh and Chuchi discussed the growing dissent against Emperor Palpatine when a Clone X trooper CX-1 attacked, clandestinely eliminating Greer before throwing a bomb at the senators. Rex grabbed it and tossed it out of their room, causing an explosion that blew 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 assailant. The clones then traveled on a shuttle through hyperspace with CX-1. Rex and Howzer discussed the object they have recovered from their prisoner, a data puck. Rex then told him to make arrangements for Fireball to examine the object at base camp at the B'omarr Order Monastery on Teth.
After capturing the assassin, the Clone Underground brought him back to the B'Omarr Order Monastery to be interrogated. However, the clone proved to be resistant to interrogation, frustrating the Underground members who considered him the only way to discover the location of Tantiss Base. Increasingly desperate, Howzer insisted that they needed to call in Clone Force 99, a unit of genetically defective clones retired to the planet Pabu, since one of their members, Crosshair, was also imprisoned on the Base and Howzer suspected him to know about its location due to his previous Imperial affiliation. However, another assassin was deployed to Teth in 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 genetically defective clone Omega in the compound. In the ensuing 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 fled into the jungle, where they were cornered by the Strike Team. Rex, recognizing Wolffe, pleaded with him to realize 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.
- Star Wars: Dawn of Rebellion: The Visual Guide