For this ask game. Still taking requests.
After separating from Ahsoka in the aftermath of Order 66, Rex goes looking for a way to save his brothers from the hell of being nothing more than meat clankers. He comes across a scientist who is on the run from being conscripted into the Imperial bureaucracy, and saves the scientist from being run down because the whole process gives Rex flashbacks to what Fives went through.
It turns out the scientist, a Twi’lek named Doctor Faesta Snamis, has been experimenting with how sound waves influence technology and the Empire wants to utilize her research by turning it toward military applications. Since Faesta, whom Rex takes to calling “Doc”, refuses to see even more destruction wreaked upon the galaxy (and Ryloth in particular, given that it was devastated by the battles fought over it by the Republic and the Confederacy), she’s been running from not just the Empire, but others too who wish to use her work for destructive means. Rex thinks she’s too idealistic, but feels obliged to help her out (it sticks it to the Empire in some small way, practically the only way he’s managed since he and Ahsoka fled Mandalore).
So lots of crazy shit happens and Faesta finds a way to use her research to neutralize the chips in the clones’ minds. They do this on a small scale at first, but then Rex starts getting ideas (boy does he get ideas). He, Faesta, and a crack team of clones who are really fucking pissed off at the Empire for turning them into flesh droids, at the Republic for making them slaves in the first place, and the Sith who have taken over, find a way to hack the Holonet and deliver the knockout punch that deactivates the chips and also manages to deliver a message to the various clone units on what’s happened – the Sith have taken over, etc. They are then encouraged to either get out, or, if they want to do something about it, start tearing the Empire down. A few end up taking the first option, completely traumatized and just can’t take it anymore, but the majority are pissed off enough to want to finish what they started.
Essentially, there is a massive military coup. Palpatine and Vader may be powerful, but even the strongest lions can be brought down by the coordinated attack of a hyena pack (or just insert an appropriate GFFA analogy here). Tarkin is found and shot, field execution style, along with a lot of other leading Imperial figures and leaders.
There are some serious tensions in the aftermath, because the clones are very distrusting of politicians, even the ones with good reputations like Bail Organa and Mon Mothma. As far as many of the clones are concerned, they colluded in keeping the brothers as slaves in a desperate attempt to preserve the Republic, along with the Jedi.
It’s Faesta who steps up and does her best to talk everyone down. She’s always believed in peace, hoped for better times once the war ended, but found herself in even worse straits as time passed. She may not have the deep understanding of being used as fodder like the clones do, but she knows oppression. She and Rex were the ones who found a way to free the clones from their chains. Now she asks them what they really want to do now that their chains are off and the primary culprits are themselves either dead or fettered in chains of their own? Continue the cycle and thus see more blood spilled, blood of their brothers, blood of innocents?
Faesta freely admits that there are no real good answers to the shitty situation they’re in. She just asks that the clones, that everyone, look for answers that don’t involve doing their level best to kill one another.
The story gets left a little open-ended, letting readers decide for themselves how things go. The clones have control at the end, but it’s control by the barrel of a blaster, and hardly sustainable, but they’re just so angry at everyone. Will Faesta’s words be enough to bring peace, when the words of so many others failed?