When Order 66 was issued by Chancellor Palpatine near the conclusion of the Clone Wars, the Jedi Order became targeted for extermination while Palpatine brought a swift end to the Old Republic by declaring himself emperor of the first Galactic Empire. The remaining Republic commandos were rechristened as Imperial commandos and incorporated into a special forces unit attached to the 501st Legion, under the command of the Sith Lord Darth Vader. However, a minority of commandos refused to comply with Order 66, either out of sympathy for the Jedi or due to other personal reasons. For instance, Ion Team did not carry out the command to kill their Jedi officers, believing it to be an invalid order, and instead opted to ensure the survival of General Roan Shryne. Other commandos fled to Mandalore, choosing to go into hiding rather than serve as the enforcers of the Emperor's New Order.
Soon after the Kaminoans began developing the Galactic Republic's secret clone army on their homeworld of Kamino, a special forces unit was conceived as a necessary addition to the overall operational effectiveness of the new military force. Jango Fett, a Mandalorian bounty hunter and the genetic template for the entire clone army, was confident that progeny would be engineered into the best soldiers in the galaxy, but also knew that there were situations that regular infantry was not suited for. As a result, he requested for a special batch of clones that he would personally train as Advanced Recon Commandos. The Kaminoans reluctantly agreed, but due to their disappointment in the failed prototypes, they felt little confidence that the second generation of ARC troopers would meet their expectations. Thus, they compromised with Fett; the bounty hunter would be allowed to train his ARC troopers while the Kaminoans proceeded with their plan to create the clone commandos, otherwise known as Republic commandos. Unlike the ARC troopers, the Republic commandos would be more loyal and susceptible to following orders without question, yet they would still retain greater ability for independent thought than the standard clone troopers. Thus, they were to be the perfect balance between two extremes. With a greater capacity for independent thinking, the commandos would be better suited to handling delicate missions with complicated objectives. If necessary, they would also be capable of devising their own way for completing missions. By being indoctrinated with absolute loyalty to the Republic, the commandos would not be difficult to control as the notorious Null-ARC troopers were.
The first batches of clone commandos were separated into squads, also known as "pods", of four clones each, in reflection of the native aiwha hunting pods from Kamino. In addition to being subjected to the computerized flash-training program, the commando squads were divided amongst the Cuy'val Dar, a group of professional mercenaries covertly brought to Kamino and hired to train the commandos in a variety of ways, such as teamwork, infiltration methods, demolition techniques, assassination and much more. The majority of the trainers were Mandalorians, such as Kal Skirata and Walon Vau; the rest were mercenaries of different backgrounds. Although Fett's Cuy'val Dar were primarily responsible for the commandos' training, Kaminoan scientists personally oversaw the development of their creations as well. Taun We took a vested interest in the training of Delta Squad's leader, RC-1138, and helped to guide him throughout the first ten years of his life.