Okay, sorry if this is, like, too soon for your worldbuilding in the Squad Spouse AU but I NEED to know how Palpy’s Plot gets ruined by the Spouses™️
I don't think it's too soon at all! The Squadron Spouse AU is likely one that I'll explore non-chronologically, so I have no issue in talking about how it's going to royally FUCK with the canon of Order 66 ahead of writing anything about it specifically in a fic.
This post is also a LONG boy so it's going under a readmore, but I promise it's worth the perusal!
The problem begins with the fact that the Companion Program was created and approved by the Galactic Senate entirely without intervention from Palatine himself. It's a rogue variable, a completely unplanned part of the war, but the most dangerous thing is that Palpatine completely disregards it as being completely beneath him and his grand scheme.
So, how does it get through the Galactic Senate? In this AU, the senate and larger public eye has a semblance of sympathy for the clones even at the start of the war--maybe it's because of a rogue journalist, or maybe its just because the clones are seen as the military slaves they honestly are in the existing canon to begin with.
"Companionship is the right of any sentient being," one senator perhaps had argued, "And as long as there are people willing to make use of their skills in medicine, psychology, emergency first aid and so on, then there is no reason they can't be an asset to the Republic and a companion to its army."
The Companion Program is shuffled through the senate one way or another, and soon it becomes apparent that a large number of civilians are plenty happy to join--largely those from less wealthy or safe-guarded planets, though there's a multitude from Coruscant that apply to be part of the program as well. The applicants that make it through are those who are fairly well-prepared to deal with the fact that they are the equivalent of deployed military dependents, but it is that exact same situation that makes them a prominent culture of people within the Grand Army of the Republic.
Stress can do a lot of things to people, but in the case of war and armies, it often builds a sense of camaraderie that is impossible to develop elsewhere. Members of the Companion Program (soon casually called 'spouses') often get to know one another very well--and an entire network of relationships between spouses and the clones they're assigned to is woven from loose threads into an entire, intricate tapestry that stretches from one side of the galaxy to the other.
And it was this very network that Palpatine didn't expect--a group of people that cared about one another and the clones they had been with (for some spouses, since the start of the war), and it didn't take long before a rumor would come rumbling through: there's something wrong, stories of nightmares weaving with the offhand report of a clone who had gone berserk and tried to kill a Jedi, one spouse going missing when they tried to investigate the cause of a strange recurring headache a member of their squadron was experiencing.
It's one little piece of the puzzle after another, coming together until the conglomerate of the Companion Program--which was filled with admittedly experienced civilians across all walks of life, not to be underestimated by any means--learned the secret. The horrible, atrocious secret that was Order 66 and the implant of a control chip inside every clone that came out of Kamino; this discovery would be entirely hushed, kept to only the few who could be trusted with it while general knowledge continue to grow in what they could do to try and stop this from happening.
Spouses with medical knowledge and training enough to be allowed to operate the surgical wards started organizing secret operations to remove chips, while others passed on information they had gathered from the chips itself--going back to Kamino, to a dark plot, an order yet to be given by the very Chancellor himself.
Not every clone is able to be saved when it comes time for Palpatine to send out the call for Order 66. But, by that time in the war, when so many had done so much work in order to stop it, it means that scarcely any Jedi are killed, the clones in majority are spared from their waking nightmare, and Darth Sideous himself is exposed and tried for his crimes against the Republic.
What does this mean for the world afterwards? Who knows! I'd like to say that Anakin doesn't ever betray the order and instead goes on to try and reform some of their doctrine with backing from many others of his peers. The clones are slowly merged into the civilian populace, though not without plenty of challenges to be explored. It's not a perfect ending, but it's at least a better one!
