When Palpatine issued Order 66, directing all of his clone troopers to betray their Jedi masters, the whole Jedi Order was decimated in an instant. But many of the clones had grown attached to their Jedi masters in their short time in the universe, and executing them was the last thing they wanted to do. Some clones managed to disobey the order to spare their comrades, while others merely missed the order’s execution.

All clones were created with a biological inhibitor chip implanted into their brains. These chips were originally the idea of Jedi Master Sifo Dyas as a contingency in the event a Jedi should go rogue. The chips were, however, repurposed once the Sith took control of the project to force them to thoughtlessly follow order 66.

In canon, there are only a few clones, that we are aware of, who have successfully removed their chips. Rex, commander of the Republic’s 501st Legion, had just sieged Mandalore and captured Darth Maul alongside Ahsoka Tano when he was ordered by Sidious to execute order 66. He was given special orders to kill Ahsoka, despite the fact that she was no longer affiliated with the Jedi Order. Disturbed by the thought of murdering his close friend, he tried to suppress the urge to kill, but inevitably his will buckled and he began shooting. After evading this attempt on her life, Ahsoka devised a plan. With the help of some astromech droids, she stunned Rex and had his inhibitor chip removed. The pair faked their deaths and parted ways, both retreating to the outer rim to live in exile.

Rex then met with commanders Wolffe and Gregor, both of whom had removed their inhibitor chips at some unknown point during the clone wars. Though it has been suggested by one Clone Wars writer that Wolffe did in fact adhere to order 66. Riddled with the guilt of his actions, he subsequently removed his chip.

Together the three of them lived in a modified AT-TE on the desert planet of Seelos. A few years prior to the Battle of Yavin, the trio were visited by the rebel Spectre cell, who requested their support in battling the Empire. Initially rejecting the offer, Rex soon changed his mind after an Empire assault destroyed their home. Wolffe and Gregor remained on Seelos and salvaged an AT-AT walker from the battle to convert it into their new home.

Clones with genetic mutations were usually immune to order 66, as a result of their mutations interfering with the function of the inhibitor chip. Experimental Unit Clone Force 99, better known as the Bad Batch, was a special forces unit initially consisting of four clone commandos that were designed with genetic enhancements. But ultimately they were a squad for clones that broke the mold, and would later take in a genetically normal fifth member.

The Bad Batch were deployed on Kaller, aiding Jedi General Depa Billaba and her padawan Caleb Dume, when order 66 was issued. Depa Billaba was gunned down, while Dume fled the slaughter. The majority of the Bad Batch were resistant to the order due to their genetic mutations. Echo, the genetically normal fifth member, was also immune as a result of his cybernetics interfering with the chip. However one member, Crosshair, was partially affected by his inhibitor chip. It did not completely corrupt his mind, but his free will was limited, and he began shooting at Dume. Crosshair was knocked unconscious and Dume managed to escape with his life.

Within days of the Empire’s creation, the Bad Batch would flee its grasp, with the exception of Crosshair. Despite having his inhibitor chip removed after order 66, he remained loyal to the Empire after questioning the Bad Batch’s purpose.

The squadron that executed Depa Billaba during order 66 was led by clone Commander Grey. In the days that followed, Grey and his unit hunted the escaped padawan, Caleb Dume, down. Grey’s conscience weighed on him during this time as he questioned the validity of the order. Eventually the padawan was captured. The unit were going to execute Dume when Grey distracted them for long enough for Dume to escape. Grey blasted the ship’s controls, disabling them and causing the ship to crash, consequently redeeming himself for his actions during order 66.

Finally we have Kix, a clone medic from the 501st Legion. After seeing Tup seemingly lose his mind and murder Jedi Master Tiplar at the battle of Ringo Vinda, Fives informed him of a scheme he had uncovered to kill the Jedi. Upon acquiring this information, Kix became curious and commenced his own personal investigation. He eventually confirmed what Fives had told him, but the separatists captured him before could notify the Jedi, putting him in a stasis pod for transportation to Count Dooku.

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