Star Wars' OTHER Order 66 Was More Twisted Than the Jedi Purge
While most Clone Troopers were brainwashed to follow Order 66, Jango Fett's ARC Troopers had a different secret directive to use on other clones.
The Star Wars saga’s Jedi Purge began with Order 66, but Jango Fett secretly gave a small group of clones a different contingency to use on other Clone Troopers. In the defunct Star Wars Legends continuity, Jango Fett oversaw the training of all of his Clone Troopers but personally trained the 100 Alpha-class ARC Troopers, who were the most formidable clones in the Republic military. ARC Troopers were fundamentally different from the rest of the Clone Army, including their own secret orders to kill their brethren if Kamino ever fell to the CIS.
In both modern canon and Legends, the Star Wars saga’s Clone Troopers are good men who believe in fighting for democracy and genuinely care for both the Jedi they serve and the people they protect. Despite this, Clone Troopers have dormant programming to kill the Jedi and establish an oppressive fascist regime once Order 66 is issued. In canon, their unwilling compliance is ensured through a brain implant, while Legends implies that they’re simply subjected to a particularly intense amount of indoctrination to follow Order 66. ARC Troopers are unique among Clone Troopers in lacking the same behavioral tampering, but they nevertheless follow contingency orders.
The secret directive given to ARC Troopers is revealed in the fiftieth issue of Star Wars: Republic, by John Ostrander, Haden Blackman, Scott Allie, Jan Duursema, Stephen Thompson, and Tomás Giorello. During the Battle of Kamino, the ARC Trooper Alpha-17, observing that the CIS forces are gaining the upper hand in their attack on the Republic’s cloning facilities, nearly destroys the laboratories, killing all untrained or unborn Clone Troopers. Alpha’s rationale is that the clones can only grow up loyal to the Republic and never fall into the hands of CIS forces, revealing that Jango Fett instructed his ARC Troopers to plan for the worst in case Kamino was ever invaded.
While canon ARC Troopers are simply ordinary Clone Troopers who receive a specialized rank and title for exemplary performance on the battlefield, Legends-era ARC Troopers lacked most of the modifications made to the rest of the Clone Army, making them more like Jango Fett than their ordinary brethren. Anakin Skywalker, who typically befriends Clone Troopers in both continuities, notes that Alpha is “rude” before the two eventually warm up to each other, showing how atypical the ARC Troopers are. While the Jedi purge was twisted, it was at least something the Clone Troopers couldn't help, while the genocide of their kin was an order they had to choose to carry out.
Clone Troopers are among the best non-Force sensitive warriors in the galaxy, and the Republic held back the overwhelming numbers of the CIS almost exclusively due to the sheer skill of the clones and their Jedi leaders, so the CIS potentially co-opting Jango Fett clones for their military would indeed be catastrophic for the Republic. Even so, ordinary Legends-era Clone Troopers would be hesitant to kill their own brothers, even with their modifications, but the largely unmodified ARC Trooper Alpha was willing to carry out the order with cold efficiency, even knowing the weight of his actions. This shows that the ARC Troopers truly embodied the ruthlessness of Jango Fett as one nearly carried out a secret variant of the Star Wars saga’s infamous Order 66 against his own brethren.