Order 66 was a pivotal command issued in "Star Wars: Episode III – Revenge of the Sith," which led to the near-extermination of the Jedi Order by the Galactic Republic's Clone Troopers. In the context of the Clone Commando units, which were elite soldiers trained for various operations, Order 66 posed a unique challenge due to their specialized training and loyalty to their commanders.
Clone Commandos, such as the characters from the "Star Wars: Republic Commando" series by Karen Traviss, often had more personality and independence compared to regular Clone Troopers. While they were still programmed to follow orders, the execution of Order 66 varied among different clones due to individual experiences and relationships with Jedi.
Some Clone Commandos, like Delta Squad, demonstrated personal loyalty to their Jedi commanders and were conflicted about carrying out the order. This loyalty often led to significant character development and ethical dilemmas, revealing the complexity of the clones' existence as both soldiers and individuals.
In various expanded universe materials, some Clone Commandos actively resisted Order 66, and the aftermath of the order's execution explored themes of loyalty, betrayal, and the moral implications of their programming. The fallout of Order 66 significantly impacted the narrative arcs of many characters within the "Star Wars" universe.