Clone Commander
Clone Commanders, also known as clone trooper commanders, represented a rank within the Grand Army of the Republic. This position was held by clone trooper officers who were in charge of regiments, each composed of 2,304 troopers. Within each corps, the sixteen clone commanders reported to their respective Jedi General.
Those Advanced Recon Commandos who held command positions were designated as Clone ARC Commanders. It was also possible for clone trooper pilots to serve as commanders. During the Clone Wars, Clone Commanders operated under the authority of Jedi Generals and, like their clone comrades, engaged in combat against the Confederacy of Independent Systems. As the war neared its conclusion, Supreme Chancellor Sheev Palpatine issued an order for all clones to turn against and eliminate their Jedi officers.
This rank persisted within the Imperial Military during the initial years of the Galactic Empire, as the clone troopers transitioned into the first generation of stormtroopers.
Description
Overview

The Clone Commander, also known as a clone trooper commander, was a military rank awarded to certain clone trooper officers during the Clone Wars and the early part of the Imperial Era. This rank was utilized by the Grand Army of the Republic, as well as the Republic Navy and the Republic Starfighter Corps. Within the structure of the Galactic Republic, the Clone Commander rank could be assigned to clone trooper officers who also functioned as special ops clone troopers, Biker Advanced Recon Commandos, Clone SCUBA troopers, Advanced Recon Force Scout Troopers, and others.
Moreover, clone trooper pilots and navigation officers were also eligible to hold this rank, commanding spatial operations instead of ground-based units. Clone Commanders could also be important enough to have their own personal guard details, consisting of two lower-ranking clone troopers who would march behind them to protect their officer. The rank was later adopted into the Imperial Military in its early stages, which was initially composed primarily of clones. Even during the early phases of Project War-Mantle, this rank remained in use over recruited Elite Squad Troopers. However, as the Imperial Era progressed, the authority of Clone Commanders began to be superseded by that of recruited officers; for example, a recruited lieutenant could delegate tasks and issue commands to a Clone Commander.
Training
Generally, Clone Commanders in the Republic Military underwent ARC training, although some, like Ponds, did not receive this particular training. Nonetheless, even without ARC training, Clone Commanders could still be trained by experienced instructors and specialize in areas such as military reconnaissance. Clone trooper officers were selected for a training program focused on facilitating effective communication between Jedi Generals and their clone trooper subordinates, although some Clone Commanders might not have been included or briefed on how to interact with Jedi high command.
Equipment

Initially, Clone Commanders within the Army of the Republic were equipped with standard Phase I clone trooper armor, distinguished by four yellow circles on the left chestplate, along with a yellow stripe running vertically down each arm, up the center of the helmet, and horizontally around the visor.
As time went on, Clone Commanders, along with other clone officers, began to customize their armor with additional gear, including kamas, pauldrons, rangefinders, secondary communication antennas, visors, jetpacks, pistol holsters, macrobinoculars, bandoliers, rank insignia plaques, integrated lights, primary communications antenna, unit affiliation markings, and more. Jaig Eyes could also be added to the commander's armor. The Phase II clone trooper armor offered even greater possibilities for modifications. Clone Commanders serving in the Republic Navy were provided with a blue cloth fabric uniform, black gloves, and a rank insignia plaque.
Galactic Republic
Grand Army of the Republic

The Clone Commander rank represented the highest level a clone trooper could achieve, outranking a Clone Captain. There were several variations of this rank, including Clone Marshal Commander and Clone ARC Commander, reflecting the diverse positions and responsibilities held by Clone Commanders. A Clone Marshal Commander served as the commanding officer of a corps within the Grand Army of the Republic, examples being Cody of the 7th Sky Corps, Bacara of the 21st Nova Corps, Neyo of the 91st Mobile Reconnaissance Corps, and Bly of the 327th Star Corps. Other commanders who led a corps included Gree of the 41st Elite Corps and 9th Assault Corps.
Clone ARC Commanders were Advanced Recon Commandos who held the rank of Clone Commander. Multiple ARC Commanders could be part of the same unit, as exemplified by ARC Commanders Blitz, Colt, Havoc, and Hammer from the Rancor Battalion. Clone officers could be promoted to Clone Commander and placed in command of half a legion or a full division. A typical Clone Commander was in charge of a full regiment, which consisted of sixteen companies. One such commander was Tacks, who served throughout the Clone Wars.

Clone Commanders could also lead smaller military units like battalions, composed of four companies. Examples include Wolffe of the 104th Battalion, Jet of his own special operations battalion, and Crane of the One-Eighty-Fourth. Clone Commanders also had the option of commanding small, specialized companies, such as a company of Clone SCUBA troopers. Clone Commander Monnk commanded a company of these troopers during the Clone Wars. Commanders like Ponds, who did not receive training to serve directly under Jedi Generals, could still be appointed as their second-in-command. Ponds also commanded Lightning Squadron, a light ground cavalry squadron.
Republic Navy and Starfighter Corps
Clone Commanders also served within both the Republic Navy and the Republic's Starfighter Corps. A clone trooper pilot known as Davijaan, or "Odd Ball," held the rank of Clone Commander. Clone Commanders could be the commanding officer of a Venator-class Star Destroyer or be part of its crew. In addition, Clone Commanders were capable of leading an entire flight group, which included multiple squadrons and flights.
Galactic Empire

The Clone Commander rank was maintained within the Imperial Military during the early years of Sidious's reign as Galactic Emperor, as the clones continued their military service as the initial generation of stormtroopers. Soon after the Galactic Republic transformed into the Galactic Empire, certain Clone Commanders were selected to lead new experimental, non-clone units made up of volunteers and conscripts. The first Elite Squad, consisting of four Elite Squad Troopers, was one such unit and was led by Clone Commander Crosshair. The clone commando Scorch also served as a Clone Commander within the Advanced Science Division.
History
Clone Wars

Clone Commanders received their training from Jango Fett, the clone template for the Republic's clone forces. Their first combat deployment was during the First Battle of Geonosis, where numerous Clone Commanders participated. Although members of the Jedi Order did not officially hold rank within the Republic Military at the time, the clone troopers and their commanders served under the Jedi who acted as de facto generals on Geonosis. During the battle, Commander CT-411 reported to Jedi Master Mace Windu, who assumed command of five special commando units. While Windu and other Jedi were on the battlefield, leading clone troopers against an army of battle droids, Grand Master Yoda oversaw the battle from the forward command center, where a Clone Commander kept him informed about the Republic Army's progress. Yoda praised the commander after he reported that the Separatist Droid Army was retreating.
Following the fall of Geonosis, the Grand Army of the Republic gathered on the Republic capital of Coruscant. Supreme Chancellor Sheev Palpatine, along with members of the Galactic Senate, observed the newly formed Republic Military as Clone Commanders and their troops boarded Acclamator-class transgalactic military assault ships, preparing to deploy across the galaxy to engage the forces of the Confederacy of Independent Systems.

Clone Commanders were assigned to Jedi Generals after the Jedi took on leadership roles within the Grand Army of the Republic. As they served together throughout the Clone Wars, relationships based on trust and respect developed between the commanders and their generals. General Obi-Wan Kenobi and Commander Cody worked together as commanding officers of the 7th Sky Corps, which included the 212th Attack Battalion. Cody displayed a strong sense of loyalty to Kenobi, who regarded the Clone Commander as a highly capable officer.
Clone Commander Wolffe and Jedi General Plo Koon also served together throughout the Clone Wars. Although the clones viewed themselves as expendable due to their artificial nature, Koon valued their lives and was willing to risk his own to protect them. This led to a close bond with Wolffe. Under their leadership, the Wolfpack became one of the most well-known clone trooper squads in the Grand Army of the Republic.
Treason and purge

Despite Admiral Wilhuff Tarkin's reservations about leadership within the Republic Military, Clone Commanders and Jedi Generals continued to lead the armies of the Galactic Republic as the Clone Wars entered their final year. The Republic's strategy shifted to eliminating the remaining Separatist forces in the Outer Rim Territories. Clone Commander Bly and Jedi General Aayla Secura oversaw the campaign on Felucia, while Clone Commander Bacara and Jedi General Ki-Adi-Mundi led the Republic assault on Mygeeto. Other battlefronts included Saleucami, where Clone Commander Neyo served alongside Jedi General Stass Allie, and Bracca, a Mid Rim planet that the 13th Battalion invaded under the command of Jedi General Jaro Tapal and his Clone Commander.
Following the Battle of Yerbana, Jedi General Anakin Skywalker committed half of the 501st Legion to the Siege of Mandalore, forming the 332nd Division, while the remaining forces returned to the Core Worlds to defend the capital during the Battle of Coruscant. The 332nd was created in response to Skywalker's former Padawan, Ahsoka Tano, who supported Lady Bo-Katan Kryze's efforts to reclaim Mandalore from the rogue Sith Lord Maul and his Mandalorian super commandos. However, because Tano had declined to rejoin the Jedi Order, she relinquished her rank as a Jedi Commander and could not officially lead Republic soldiers. As a result, Skywalker promoted his second-in-command, Rex, to the rank of Clone Commander, granting the former Clone Captain the authority to lead the new division.

Following the successful defense of Coruscant, Clone Commander Gree and the 41st Scout Battalion accompanied Jedi Generals Yoda and Luminara Unduli to Kashyyyk, with the intention of protecting the strategically important homeworld of the Wookiee species. After Yoda's departure, Cody and Kenobi deployed their battalion to Utapau, where General Grievous had retreated following Count Dooku's death. However, after the Jedi High Council's failed arrest of Chancellor Palpatine—who was revealed to be the Sith Lord Darth Sidious—after Grievous's destruction during the Battle of Utapau, the chancellor ordered the Clone Commanders and their clone troopers to execute Order 66, turning the Jedi's own army against them.
With the exception of the genetically defective clones of Clone Force 99, the behavioral modification biochips implanted within their brains compelled the majority of standard clone troopers to comply with Order 66, including the Clone Commanders who had worked closely with the Jedi Generals. Across the galaxy, the Jedi were killed by the soldiers and commanders they trusted, including Mundi, who was killed by Bacara, and Secura, who was fatally shot in the back by Bly and his troops.

Sidious also gave strict orders to the Clone Commanders to execute any clone trooper who defied his plan to systematically purge the Jedi Order. However, Rex's biochip had been surgically removed, allowing him to defend Ahsoka Tano against his own soldiers, who were still under the control of their programming. Subsequently, his subordinate Clone Lieutenant Jesse accused him of treason against the Republic and declared that Rex would be demoted from the rank of Commander and executed. In response, Rex told Tano that he had never liked being a Commander anyway. After becoming a fugitive from the Empire, which officially declared him dead, Rex reverted to his former rank of Captain.
Changing of the guard

In the days following the formation of the Galactic Empire, the rank of Clone Commander was given to Crosshair, the only member of Clone Force 99 who remained loyal to the Galactic Empire. To assess the early results of Project War-Mantle, Admiral Tarkin instructed Commander Crosshair to take a squad of enlisted soldiers to Onderon and eliminate Saw Gerrera's insurgents.
ES-01, one of the natural-born human soldiers in Crosshair's squad, questioned the clone's fitness to be a commander, particularly since the Empire had already begun the process of decommissioning the clone trooper program. However, Crosshair asserted his authority by executing ES-01 for refusing to complete the mission, which involved killing the civilians traveling with Gerrera's group. The squad's success reinforced Vice Admiral Rampart's belief that the Imperial Army could be molded into the most powerful fighting force in galactic history, provided that non-clone soldiers continued to learn from the experience of veteran clones like Commander Crosshair.
Several months into the Empire's reign, Clone Marshal Commander Cody led a unit of clone stormtroopers in quashing a Separatist holdout on the planet Desix. Crosshair, who had returned to the Empire after being abandoned on Kamino during the Imperial withdrawal and attack and had been stuck on the planet for thirty-two planetary rotations, was assigned to the squad. Although he initially assumed he would be leading the squad, Crosshair was not yet cleared to resume command but was happy to work under Cody once more. However, Cody would desert after the mission, having become disillusioned with the Imperial cause.
Around 18 BBY, Clone Commander Mayday was killed in action during a failed attempt to recapture Imperial supplies stolen by insurgents on the planet Barton IV. Mayday's death proved to be the final factor in Crosshair's own loss of loyalty to the Empire. Clone commando Scorch served as a Clone Commander in the Advanced Science Division but was killed during the skirmish on Wayland.