During the Clone Wars, within the Grand Army of the Republic, certain Jedi held the position of Jedi Commanders. These officers of the military were appointed shortly after the First Battle of Geonosis in 22 BBY, which marked the beginning of the Clone Wars. The title was bestowed upon the Padawans belonging to the Jedi Order. Holding the rank of commander gave them command over the clone troopers within the Grand Army, including clones of higher rank, such as Clone Captains. However, just as in the Order itself, these Jedi Commanders were under the authority of the Jedi Generals, those veteran Jedi who had completed their training and achieved the ranks of Jedi Knights and Jedi Masters.
Although occasionally dispatched on solo missions, Jedi Commanders often fought alongside their masters, who were also generals. As the war between the Galactic Republic and the Confederacy of Independent Systems neared its conclusion in 19 BBY, most Jedi officers faced betrayal and death at the hands of their clone troopers due to Order 66, a military directive that branded all Jedi as enemies of the state. While many Jedi perished during this subsequent purge, some managed to escape into hiding, including Commander Caleb Dume and former Commander Ahsoka Tano. Both later became key supporters of the Alliance to Restore the Republic during the reign of the Galactic Empire.
The Jedi Military Integration Act established the rank of commander and assigned Jedi Padawans as second-in-command to the Jedi Knights and Jedi Masters who held the rank of Jedi General, thereby commanding the clone trooper forces of the Grand Army of the Republic. A Jedi Commander held a higher position than all clones, with the exception of Clone Commanders. Jedi Commanders were subordinate to the higher-ranking Jedi General, but they were granted authority over clone forces as large as a regiment. Clone troopers were conditioned to obey orders without question and would carry out commands given by their Jedi Commanders, just as they would with their Jedi Generals.
The Grand Army of the Republic was first used in battle against the Separatist Droid Army of the Confederacy of Independent Systems during the First Battle of Geonosis in 22 BBY. At this time, the Jedi Order did not have formal standing within the military forces of the Galactic Republic. Nevertheless, the clone troopers obeyed the Jedi, who functioned as de facto generals on the battlefield. Following the Battle of Geonosis, the clones began to informally address Jedi Knights and Masters as generals, with their Padawans holding a lower rank.
As the war expanded and Padawans became involved in skirmishes, Supreme Chancellor Sheev Palpatine suggested to the Jedi High Council that Padawans be officially integrated into the military, leading to debate within the Council. After the mission to Cato Neimoidia, the Galactic Senate passed the Jedi Military Integration Act, formally designating fully-trained Jedi as generals. Meanwhile, Jedi still undergoing training as Padawans were granted the official, but lesser, rank of commander. Many citizens of the Republic were perplexed by the sight of teenage Jedi Commanders leading fully grown clones. However, many were unaware or had forgotten that the Padawans were chronologically older than the clone troopers due to the clones' accelerated growth.
Ahsoka Tano was assigned to Anakin Skywalker, who had recently become a Jedi Knight, during the Battle of Christophsis. This made her Skywalker's official Padawan, even though he was reluctant to train a new generation of Jedi. As a result, Tano also became a Jedi Commander in the Grand Army of the Republic. On Christophsis, she fought alongside the soldiers of her master's unit, the 501st Legion, and continued to serve as Skywalker's second-in-command in numerous battles throughout the galaxy, including Teth, Bothawui, and Ryloth. In 21 BBY, Tano collaborated with Commander Barriss Offee, the Padawan of Jedi Master Luminara Unduli, to destroy the Geonosis primary droid foundry during the Second Battle of Geonosis. Following the Republic's victory on Geonosis, Commanders Tano and Offee worked together to prevent the spread of a brain_worm infestation that had infected the crew of the Pelta-class frigate TB-73.
In 20 BBY, Commander Knox perished in battle along with General Halsey and their clone troopers, all of whom were killed by Count Dooku's new enforcer, Savage Opress, a Dathomirian and former Nightbrother. Yigan Lam was the Padawan to Jedi Hallan Krintu, and she was present during the sabotage of a simulation chamber on Kamino. Leh'ahnyo Vas served as a Jedi Commander under her master in their clone unit.
As the war dragged on, Barriss Offee secretly became disillusioned with the Clone Wars, the Republic, and the Jedi's participation in the conflict. In 19 BBY, she masterminded a terrorist attack on the Jedi Temple on Coruscant, resulting in the deaths of several Jedi, clone troopers, and civilian workers. Furthermore, her actions led to the death of her friend, Tutso Mara, and the framing of another friend, Ahsoka Tano, whom Offee had manipulated to take responsibility for the attack. Although Offee was ultimately revealed as the true culprit and traitor by Tano's master, Anakin Skywalker, Tano declined the opportunity to rejoin the Jedi Order and the Grand Army of the Republic. However, when Tano unofficially rejoined the Republic Military to lead forces in the Siege of Mandalore to aid the Mandalore resistance, the clones in her unit treated her as if she still held the rank, out of respect.
During the final days of the Clone Wars, the clone troopers turned against their Jedi Generals and Commanders after receiving Chancellor Palpatine's order to execute Order 66. Having been labeled as enemies of the state by the chancellor, many Jedi were suddenly shot down by their own soldiers, all of whom had been programmed to carry out Order 66 without question, regardless of their previous beliefs. Cal Kestis, a Padawan who served as a Jedi Commander in the 13th Battalion, survived Order 66 thanks to the sacrifice of his master, Jedi General Jaro Tapal.
Caleb Dume, another Jedi Commander, survived the clones' betrayal because his master, Depa Billaba, gave her life to protect Dume from the blaster fire of their battalion. During the reign of the Galactic Empire, the few remaining Jedi were forced into exile to escape the purge that nearly destroyed their Order. Before the Galactic Civil War, former Jedi Commanders Dume and Tano joined the Alliance to Restore the Republic during its early years as a resistance movement. Dume, now known as "Kanan Jarrus," continued the Jedi tradition by training Ezra Bridger of Lothal, a Force-sensitive individual, as his own Padawan.