The trailer for the upcoming Star Wars animated series, Star Wars: The Bad Batch, strongly implied that the commandos of Clone Force 99 didn't obey Order 66. Although the clone troopers have free will and a unanimous belief in democracy and altruism, their tragic ultimate purpose was to help wipe out their Jedi allies and usher in a fascist coup. As embryos, all clone troopers are given a brain implant that, when Order 66 is activated, erases their free will and compels them to kill Jedi for the Galactic Empire. The members of Clone Force 99 may have been able to retain (or regain) their free will through various means.
Clone Force 99, nicknamed the “Bad Batch,” debuted in the first four episodes of Star Wars: The Clone Wars season 7. As described by Commander Cody, these commandos were born with mutations that the Kaminoans and Republic military found useful. Each clone demonstrates unique abilities that make them far more formidable than most humans, even their standard clone trooper brethren. Moreover, they demonstrate far more independent thought and behavior than the rest of the Clone Army. This led many viewers to question whether or not they would follow Order 66, and if not, how they’d resist their control chip implants.
At the start of the latest Bad Batch trailer, Admiral Wilhuff Tarkin notes both the fighting prowess and the chronic disobedience of Clone Force 99. Later in the trailer, the Clone Commandos are shown fighting standard clone troopers (blasting their weapons rather than the troops themselves) and escaping Kamino, with Tarkin demanding that the Bad Batch be found and eliminated. The trailer also shows the Bad Batch working alongside Captain Rex, who notably regained his free will and aided Ahsoka Tano in the series finale of The Clone Wars. These details all but directly confirm that Clone Force 99 hadn't obeyed Order 66.
There are several ways that the Bad Batch could've disobeyed Order 66. Their mutated physiologies may have rendered them incompatible with the control chips, preventing them from getting the implants in the first place. What’s more likely, however, is that they simply removed the chips before Order 66 was activated. The Bad Batch may have learned about the late ARC Trooper Fives’ discovery of the chips through Captain Rex. Given their rebellious nature, the commandos would have unsurprisingly removed the chips in secret. As for their fifth member, Echo, his chip may have been removed or rendered inoperable during his time as a prisoner of the Techno Union.
As the sequel series to The Clone Wars, Star Wars: The Bad Batch can be expected to further explore the humanity of the clone troopers, and how they were eventually replaced by the Empire’s recruited Stormtroopers. With appearances by Captain Rex, Fennec Shand, and Saw Gerrera, the series will also tie into the larger Star Wars franchise, and perhaps tie up some loose ends (such as the fate of Commander Cody). Whichever way that The Bad Batch managed to disobey Order 66, it’s clear that they aren’t loyal to Tarkin or the fledgling Galactic Empire, and will become one of the fascist regime’s first opponents.