Themes surrounding personal autonomy and what it means to be personally autonomous are very, very common in sci-fi and fantasy. Many stories explore this or at least touch on it, especially in regards to robots (some of my favorite modern ones being Fallout and Overwatch), and Star Wars is far from an exception. I think it's such a popular theme because these genres generally pose questions about ourselves and our future, and having or lacking personal autonomy is something we can all relate to- and all fear. I've recently started to make my way through Rod Sterling's The Twilight Zone, and a common theme across many of the episodes I've found is autonomy. Whether it's with robots like in "The Lonely," or when characters ability to make decisions for themselves is impaired or taken away- the loss of personal control and the fear that comes with that is a really common and fairly universal idea.
Which is why I'd like to talk about the way this theme shows up in Star Wars. While this theme seems to be touched on sometimes with droids (L3-37's story in Solo comes to mind), as well as with First Order stormtroopers and more, I'll mostly be talking about it in terms of the clone troopers, since I think that they are the best example of this that Star Wars has.
In The Clone Wars, we quickly are able to understand that the clones, while bound to the Republic and ordered around, are autonomous beings. They question and sometimes disobey what they're told to do, we see a clone trooper who betrays the Republic, and another who leaves and starts a family. It seems pretty obvious to say, but the clones are people. People created out of unusual circumstances, and used as soldiers without a choice, but still people. Clone troopers are individuals, they make their own decisions and have their own thought process.
Which makes Order 66 so much more terrifying. The idea that a chip in your brain could just totally override someone who previously had free will and personality... it's scary. The loss of autonomy that clones have because of it just adds to the horror of that already terrifying moment in galactic history. Seeing clones turn on the Jedi that they just moments ago may have been laughing and joking with. And of course there's cases like with Rex, where they clearly try to resist and it's even more heartbreaking.
The clones are, as a whole, tragic characters. They're created and exploited for violence, under the control of the Republic, and just as the war is ending and it looks like there might possibly be freedom in sight for them, their chips are activated and they lose their own free will, and are forced to gun down people they once respected, even saw as friends. The Clone Wars puts in a lot of work to make us see the clone troopers as being relatable, rather than the relative background characters they were in the prequel movies, so to see them completely lose control over themselves, forced to do something and being unable to stop it, represents the fears that we often have about lacking control over our own life.
While we don't have chips in our brains that will make us kill Jedi (probably), it's very, very common for people to be stuck in situations where they don't really have the ability to make our own choices. More often than not it's mundane situations that you probably don't even think about too hard through this lens, like your boss scheduling you to work a shift you don't want and not giving you any choice in the matter, but sometimes they can be really drastic, even dangerous. And because of the reality that this fear of losing control of one's life is unfortunately all too common, the tragedy of clone troopers just cuts us that much deeper.