The Clone Underground was an underground resistance network that fought the newly formed Galactic Empire, with their main goal being to free and shelter any disillusioned clone troopers 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. Rex and Echo, joined by many other disillusioned clones, began to strike against the Empire with their companions in order to free imprisoned clones and conduct other anti-Imperial operations.

In 18 BBY, after having their base on Teth discovered by an Imperial clone X trooper, the Clone Underground was largely annihilated in a subsequent assault by Imperial forces. Rex and his few surviving companions fled the planet after pleading with Clone Commander Wolffe, who had led the Imperial assault, to which he reluctantly allowed.

In 19 BBY, following the execution of Order 66,[8] the Clone Underground[2] was established by Rex as a resistance network.[1] The goals of the Clone Underground included helping disillusioned clone troopers escape the Imperial Military[10] and fighting the Empire in the name of the fallen Galactic Republic.[11] By 18 BBY,[12] 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.[10] The network managed to rescue multiple clones throughout its history, including Gregor, Fireball, Nemec, Captain Howzer, and two other clone troopers from his squad.[5] Additionally, Clone Force 99 member and former Advanced Recon Commando, Echo, joined the network following the passing of the Imperial Defense Recruitment Bill.[4] Rex maintained contact with and was occasionally assisted by the rest of Clone Force 99, which included Hunter, Omega, Wrecker, Tech, and Crosshair.[7]

The network possessed a ship known as the Remora that was equipped with a detachable leech vessel, as well as several captured Rho-class transport shuttles. The Clone Underground helped rescue clone troopers[5] 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,[7] though they also made use of a repair shop on Coruscant