The Special Operations Brigade functioned as a brigade-level formation within the Grand Army of the Republic, and subsequently the Galactic Empire, comprising clone intelligence and special forces personnel. During the era of the Galactic Republic, they were also referred to as the GAR special forces. Due to their adaptability and usefulness throughout the Clone Wars, the Nu-class attack/transport shuttle was frequently utilized by both GAR special forces units and Jedi alike. Within this brigade were members of the Advanced Recon Commando corps and clone commandos. The clone special operatives, including ARC troopers and clone commandos, operated as clone agents within the elite Special Operations Brigade during the Clone Wars.
During the events of the First Battle of Geonosis in 22 BBY, Clone Commander Ponds commanded five commando units. Throughout this engagement, Ponds and his commandos operated under the command of Jedi Master Mace Windu. Later that same year, during the Battle of Christophsis, several clone commandos served under the command of Jedi General Anakin Skywalker, who instructed them to hold their positions following a Separatist withdrawal.
Many clone commandos from Foxtrot Group perished in 20 BBY during the Battle of Sarrish. Later that year, Delta Squad was tasked with recovering the remains of the deceased Jedi Master Halsey and his Padawan, Knox.
Clone Force 99, an elite clone commando unit composed of genetically defective clones, was deployed on high-risk missions for the Galactic Republic and maintained a perfect success record. Known informally as the "Bad Batch," the unit was comprised of five CT-99 clones. In 19 BBY, Crosshair, a member of Clone Force 99, assumed command of the Elite Squad, which consisted of newly enlisted Imperial recruits.