Clone commandos, also known as Republic commandos during their service to the Galactic Republic, and later rebranded as Imperial Commandos under the Galactic Empire, represented the elite tier of clone troopers. They operated within the Grand Army of the Republic's Special Operations Brigade throughout the duration of the Clone Wars. These specialized soldiers were the result of genetic experimentation conducted by the Kaminoans using the Jango Fett template. These special forces soldiers were distinguished by their rigorous training and elevated status within the clone army. In 22 BBY, Clone Commander Ponds delegated control of five commando units to Jedi Master Mace Windu, who subsequently deployed them in a direct assault against the Separatist Droid Army during the First Battle of Geonosis.
As the war between the Republic and the Confederacy of Independent Systems spread across the galaxy, these commandos were structured into squads, providing crucial support to the Republic's war efforts as an elite component of the Grand Army. One such team, Delta Squad, following the battle on Devaron, directly reported to the High Council of the Jedi Order, confirming the absence of survivors at the site of the massacre. Foxtrot Group, another commando unit, was led by Clone Captain Gregor and served alongside the 212th Attack Battalion until the Battle of Sarrish, after which they were designated as "missing in action."
Towards the end of the conflict, Clone Force 99, known as the "Bad Batch," participated in the Battle of Anaxes, fighting alongside Jedi General Anakin Skywalker and the 501st Legion. Unlike the standard clones, who were genetically identical to each other and their template, the Bad Batch commandos exhibited distinct characteristics that set them apart from both the regular clone forces and from each other.
Following the Clone Wars' conclusion, the clone commandos were integrated into the Imperial Military. In the months after the Empire's establishment, many clone commandos were assigned as training instructors to TK stormtroopers, non-clone soldiers intended to reinforce and eventually replace the clone troopers entirely. Other commandos were selected to form the Imperial royal guard, a specialized unit tasked with protecting and assisting the Advanced Science Division under the direction of Royce Hemlock.
Kaminoan scientists sought to create "super soldiers." In their endeavor, they changed and augmented the genetic template of some clone troopers, who were the basis of the clone army, resulting in the army's first commando unit.

During the First Battle of Geonosis, five commando units served under Clone Commander Ponds. This battle marked the initial engagement of the newly formed Grand Army of the Republic—the army of clones created by the Kaminoans—against the Separatist Droid Army in the Clone Wars. During this time, Ponds and his commandos operated under the command of Jedi Master Mace Windu, a prominent member of the High Council of the Jedi Order. In the course of the Battle of Christophsis, several clone commandos were under the command of Jedi General Anakin Skywalker, who instructed the commandos to maintain their positions following a Separatist retreat.
Subsequently, the Jedi Council dispatched Delta Squad to investigate the massacre that had occurred on Devaron. The team recovered the body of Master Halsey, along with that of his apprentice Knox. Gregor, the Clone Captain leading Foxtrot Group, participated in the Battle of Sarrish. With the Republic forces overwhelmed by Separatist battle droids and casualties escalating, Gregor boarded a shuttle in search of reinforcements. However, he crashed on the remote desert world of Abafar. He was rescued from the wreckage by Borkus, a Sullustan male who owned Power Sliders, a diner located in the small mining settlement of Pons Ora. Gregor was listed as missing in action in the Republic Military database. He was later discovered by Colonel Meebur Gascon and D-Squad. After regaining his memories, Gregor decided to assist Gascon and his squad in destroying a rhydonium mining installation operated by the Separatists. He volunteered to remain behind to provide D-Squad with time to escape, and he ultimately survived.
During an effort to suppress an insurrection on Yalbec Prime, Clone Force 99, also known as "The Bad Batch," was summoned by Commander Cody during the Battle of Anaxes to assist him and Clone Captain Rex in discovering the secret behind Admiral Trench's strategies. The situation escalated when Wrecker, the team's bruiser, severed the Yalbec queen's stinger with a blade, causing multiple Yalbec males to attempt to mate with the clones. Nevertheless, the team managed to escape to Anaxes aboard their gunship, the Marauder.

Following their collaboration with Rex on Anaxes, the Bad Batch joined him and General Skywalker on a mission to Skako Minor to rescue the captured Advanced Recon Commando Echo. After the modifications he underwent, Echo became a defective clone trooper. After Echo's rescue, Rex, Skywalker, Echo, and the Bad Batch worked together to eliminate Trench's flagship Invulnerable and his Droid Army. After that victory on Anaxes, Echo, who was further promoted to the rank of Clone Corporal, joined the Bad Batch because of the cybernetics he was given on Skako Minor, which he felt separated him from the average clone trooper.
Prior to the Battle of Kashyyyk, the Wookiee Chieftain Tarfful was captured by Trandoshan enslavers. These Trandoshans had made a deal with Count Dooku, but a group of clone commandos rescued Tarfful from the slavers. Meanwhile, the Bad Batch maintained their perfect mission success rate, participating in the fighting in the Conquest of Kaller before the execution of Order 66. Skywalker, now known as the Sith Lord Darth Vader, led the 501st in a siege of the Jedi Temple during the execution of Order 66. Among his forces was an elite group of clone commandos, whom Vader led into the Temple alongside the standard troopers to eliminate all Jedi present within the building.

Following the Clone Wars' end and the Republic's transformation into the Galactic Empire in 19 BBY, clone commandos, now officially renamed Imperial Commandos, continued their service within the Imperial Military. In the months after the Empire's formation, fifty commandos, including Gregor, were stationed at an Imperial Base on the planet Daro to train the first generation of non-clone Imperial stormtroopers, designated as TK troopers, totaling 1,000 soldiers. As part of Project War-Mantle, the TK troopers were intended to strengthen and eventually fully replace cloned soldiers throughout the Imperial Military. Wearing new armor, the TK troopers were instructed by the clone commandos, although Captain Gregor withheld some of his knowledge. Eventually, Gregor became disillusioned with the Galactic Empire and deserted one night, but was tracked through the forests of Daro by Imperial forces, captured, and imprisoned. Despite being captured, Gregor managed to activate a homing beacon to contact former clone officer Rex, who was secretly operating the Clone Underground, a resistance network of rogue clones.
The Bad Batch—who, except for Crosshair due to his continued loyalty to the Empire, had also defected from the Empire and became mercenaries for the information broker Cid—infiltrated the base to rescue Gregor. After Gregor's rescue, the base's security protocols were triggered by Tech, who used an old clone code, Code-16, which proved ineffective at the facility. Shortly after, they were ambushed by a squad of TK troopers and their clone commando instructor. The troopers were incapacitated by stuns, and the commando was placed in a chokehold and strangled unconscious by Hunter. The group then proceeded to a turbolift to reach the base's summit and escape, but were intercepted by another squad of TK troopers and commando Scorch, who immediately opened fire. The Bad Batch managed to escape by lowering the lift and exiting, but continued to be pursued by Scorch and his TK troopers. Engaging in firefights throughout the base's corridors, Gregor was wounded by Scorch, who in turn was stunned multiple times and incapacitated. Another clone commando and his forces approached from the opposite direction, forcing the Bad Batch to escape through the base's exhaust vents that led through the mountain to an opening on a cliffside.
A clone commando and his troops determined their location and moved in on the group at the exhaust vents. The commando and the stormtroopers fired on the Bad Batch as they awaited their ship, and the commando was shot by Wrecker, who had arrived on the Marauder. As the rogue clones were escaping, the clone commando charged forward through the exhaust vent and engaged in hand-to-hand combat with Sergeant Hunter and Echo, but was restrained. After managing to break free from the hold and stepping back into the exhaust vent, the commando was accidentally struck with a barrage of blaster fire from his own troopers and subsequently fell to the bottom of the mountain, screaming. Hunter was separated from the rest of the rogue clone group during the skirmish and was captured by several clone commandos and multiple TK troopers. He was subsequently imprisoned and taken under Imperial custody.

Meanwhile, commandos with grey markings, identified as the Imperial royal guard, were stationed at the Tantiss Base in Mount Tantiss, the location of a cloning operation on the planet Wayland overseen by the Advanced Science Division. Both there and off-world, commandos in blank armor provided security for the scientific division. Royal guard commandos escorted the Kaminoan Chief Medical Scientist Nala Se to the Wayland facility, where she was greeted by the Imperial medical officer Scalder. Scorch would later be transferred to Wayland as a Clone Commander.
In 18 BBY, more than a year after the Empire's formation, an Imperial shuttle transporting a cloned Zillo Beast was pulled out of hyperspace after the cloned animal escaped containment and attacked the vessel's crew. The beast chased a lone surviving clone commando through the ship's corridors before ultimately killing and consuming him. Concurrently, royal guard commandos were present for the arrival of Doctor Royce Hemlock on Mount Tantiss, as he was appointed to lead the Advanced Science Division and all cloning operations at the facility. Upon learning that an Imperial transport carrying a cloned Zillo Beast had crash-landed on the planet Silla, Hemlock dispatched a strike team of royal guard commandos to recapture the beast. After the cloned animal was subdued and put into stasis, the clone commandos rounded up the populace of a nearby village that had witnessed the Zillo Beasts' rampage and shipped them off-world to be dealt with.
Sometime later, a royal guard commando assisted in the transfer of clone test subjects from an outpost on Balmorra to the Wayland facility on Wayland. The commando boarded a Gozanti-class cruiser along with a security team of stormtroopers and the Imperial Captain Pearce. Before the cruiser could jump to hyperspace, it was ambushed by a shuttle belonging to the Clone Underground. As the rogue clones boarded the Gozanti and fought through its stormtrooper crew, Pearce ordered the royal guard commando to erase the ship's databank to prevent it from falling into enemy hands. The rogue clones entered the ship's bridge and dispatched the commando before he could complete his task, and held Pearce at gunpoint before the Imperial officer killed himself via a suicide shocker. The rogue clones fled the ship as it was strafed and destroyed by Imperial V-wings.
During her time with the 97th Legion, which began in 2 ABY, Thara Nyende was told that her unit commander, SP-113 was one of the original clone commandos which had founded the Stormtrooper Corps. She became more convinced of the claim after 113 survived a detonation from close up in 3 ABY.

Clone commandos were outfitted with Katarn-class Commando Armor, a specialized armor set exclusively for commandos. This armor included a backpack used to store various items such as grenades and sabotage equipment. Commandos were permitted to select the colors of their [armor](/article/armor]. In combat, they used the DC-17m Interchangeable Weapon System and the DC-17 hand blaster, although the DC-15A blaster rifle used by standard clone trooper infantry and TK stormtroopers was also used by clone commandos. They also had access to thermal detonators—specifically the class-A model and its hemispherical variant—and an unidentified blaster pistol model. Their left gauntlet contained a repulsor, while their right gauntlet housed a vibroblade. Commandos could also modify their blaster's barrel to include an anti-armor grenade launcher.
The Galactic Empire's Advanced Science Division had a significant number of clone commandos, many of whom were stationed at the division's facilities, such as Tantiss Base on Wayland, and aboard its vessels, such as transport 904. Clone Commander Scorch led the Advanced Science Division's clone commando force.

During the development of the clone army, the Kaminoans experimented with the genetics of the Jango Fett template to create super [soldiers](/article/soldier]. Although the experiments yielded limited success, four of the test subjects formed Clone Force 99, calling themselves the "Bad Batch." The Bad Batch was engineered to be different, but unlike the enhanced clone commandos who came before them, each member of the Batch had a unique genetic mutation designed to heighten a specific skill set. The specialist clone commandos used their "desirable" mutations, along with unorthodox tactics, to accomplish their objectives. Members of Clone Force 99, an elite squad of defective clones, had the prefix "CT" in contrast to the "CC" or "RC" used by regular clone commandos. The group was led by Clone Sergeant Hunter, who was strong and stoic, and had greater combat prowess than most.
Wrecker provided the team's muscle, possessing extraordinary strength, though he had a temper. Tech, while not physically imposing, was a gifted strategist and unmatched in the use of technology. Crosshair was the squad's no-nonsense marksman, though he did not like working with "regs," by which he meant unaltered clones. Clone Corporal Echo, a cyborg, joined the squad after the crucial Battle for Anaxes. Though experimental, they were extremely effective during the Clone Wars.

Clone X troopers were clone commando warriors created when a clone trooper was taken to and brainwashed within Mount Tantiss, losing their prior identity in the process. Once they were trained and "activated," as trooper CX-2 put it, X troopers were deployed to carry out secretive operations during the Imperial Era, such as taking on assassination jobs. One such assassin was Clone X, who Clone Captain Rex was certain was not a Kamonian-produced trooper. Clone X denied Rex the chance to learn more about his existence by killing himself with a suicide shocker, only describing himself as a "believer" in the Imperial cause.

Delta Squad was a Republic commando squad dispatched to Devaron by the Jedi Council to recover the bodies of Jedi Master Halsey and his Padawan Knox, who had been killed there. The squad was led by Clone Sergeant Boss and included second-in-command Fixer, Sev, and Scorch. Delta Squad participated in some of the war's most dangerous missions.
The Elite Squad was composed of multiple Elite Squad Troopers that were led by a clone commando; Clone Commander Crosshair.

Foxtrot Group, an elite clone commando unit under the command of Clone Captain Gregor, served within the 212th Attack Battalion. This unit was declared missing in action following the Battle of Sarrish. Captain Gregor was also listed as missing after the same battle. However, he later resurfaced on Abafar, suffering from amnesia. He demonstrated a willingness to sacrifice himself during their escape from Abafar, vowing to return home, which he accomplished, remaining active throughout the Imperial Era. Later, after being stationed on Daro, he deserted the Empire and joined the Clone Underground.

Imperial royal guards, a substantial group of clone commandos, operated under the Galactic Empire's secret Advanced Science Division, with the responsibilities of safeguarding its facilities and retrieving its assets. They were primarily stationed at the Wayland facility located on Mount Tantiss, but could also be found at Imperial locations such as the Balmorra outpost. Most royal guard commandos were easily recognized by the gray markings present on their armor, while others opted to restore their armor to its original blank-white appearance.
As part of Project War-Mantle, which involved the training, organization, and deployment of TK stormtrooper conscript soldiers for the Imperial Army, fifty clone commandos, including Clone Captain Gregor and Scorch, were sent to the Imperial Base on Daro.
Within the Imperial Army's Recovery Strike Team, led by Clone Commander Wolffe, two clone commandos, including Clone Lieutenant Hilo, were assigned. The strike team's composition included several TK stormtroopers and a sizable contingent of clone troopers.
The concept of clone commandos was first hinted at in Star Wars: Episode II Attack of the Clones during the Battle of Geonosis. The idea was formally introduced in The Cestus Deception, a Star Wars Expanded Universe novel, and the characters were later prominently featured in the game Star Wars: Republic Commando. Clone commandos became part of Star Wars canon with the Star Wars: The Clone Wars episode "Witches of the Mist."

Concept art created by S. Carey for the Star Wars: The Bad Batch episode "War-Mantle" for both Scorch and a standard clone commando identifies clone commandos as a type of ARC trooper, with both model sheets using variations of "cloneCommandoARC" in their names. These pieces, dated April 22, 2020, were released on StarWars.com following the airing of "War-Mantle." While the Getty Images page for Walt Disney Studio labeled clone commandos in The Bad Batch episode "Shadows of Tantiss" as "Clone ARC Commando Troopers," the video game Star Wars Battlefront II and the reference book Star Wars: The Secrets of the Clone Troopers portray clone commandos and ARC troopers as distinct clone classes.