In the twelfth episode of Star Wars: The Bad Batch, “Rescue on Ryloth,” Clone Force 99’s mission to Ryloth highlighted the real programming of the Republic’s (and now Empire’s) Clone Troopers. While Hunter and most of the squad are hesitant to risk their lives to save Eleni and Cham Syndulla from Imperial captivity, Omega (an unaltered clone) convinces them to do the right thing by appealing to their programming. Meanwhile, Clone Captain Howzer agonizes over his brainwashing-induced loyalty to the Empire and adhering to his morals, leading to one form of programming overpowering the other. Both cases highlight the essential nature of the clones.
The complex and often contradictory purpose of the Clone Troopers is revealed and emphasized in numerous canon and Legends material. In Star Wars: The Clone Wars, Star Wars Rebels, and The Bad Batch, the clones are often the focus of story arcs. The Clone Army was the Sith Lord Darth Sidious's secret weapon in his plan to eradicate the Jedi and establish the Galactic Empire. While the clones’ compliance in this initiative was enforced via brainwashing, their true personalities were altruistic and friendly, with a genuine belief in the Republic’s democracy. The few clones who defied their brainwashing turned against the Empire, often joining the Rebel Alliance to restore freedom to the galaxy.
Clone Force 99 has generally focused on survival rather than overthrowing the Empire in The Bad Batch. Naturally, infiltrating Lessu and rescuing the Syndullas from the Empire seemed like too great of a risk for the now-soldiers of fortune. Omega, having grown up on Kamino and becoming the newest member of the Bad Batch, reminds Hunter that putting oneself on the line for people in trouble is precisely what soldiers do. Although Omega is unmodified and the rest of the Bad Batch have minimal mental modifications, they are all Clone Troopers at the end of the day. While the clones were secretly designed to gain the trust of the Jedi before murdering them, their “true” selves were the galaxy’s greatest soldiers, who saved countless innocent lives throughout the Clone Wars. Thanks to Omega, the rest of the Bad Batch successfully rescued Hera’s parents.
Simultaneously, the Clone Captain Howzer, who was brainwashed into Imperial service due to Order 66, dealt with a similar crisis of programming. Although his brain implant was presumably functioning, Howzer noticeably acts as most clones did in their right mind in both of his appearances. Howzer realizes that the Republic clones fought for years to free Ryloth from Separatist oppression, only to now subjugate them as Imperials. This leads him and several Clone Troopers under his command, to turn against the Empire, allowing the Bad Batch and the Syndullas to escape and getting themselves arrested in the process.
Clone Force 99’s behavior is unsurprising, given their few mental modifications and having removed their control chips, but Howzer and several of his men defying their brainwashing implants is a significant development. Previously, the control chips were shown to completely remove the clones’ free will and change their personalities for the worse. Somehow Howzer and his troopers overcame the programming and did what they felt was right. In doing so, they may suffer grave consequences, but they returned to ideal, selfless, freethinking soldiers they’d been before Order 66, and creating the possibility of more widespread clone defiance of the Empire. The clones’ “real programming” was their upbringing on Kamino and the battlefields alongside the Jedi, rendering them truly good men, and the Ryloth mission in Star Wars: The Bad Batch made this abundantly clear.
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