some of the jedi actually have their shit together re: the morality of a slave army.
Namely Aayla Secura and Plo Koon. From the start of the war, they both voiced opposition to taking part, specifically citing the clones’ situation. The Council convinced them to take part as generals anyway, on the basis that at least they could do some good for the clones as generals, whereas if they sat out and let another take their place, they wouldn’t be able to do anything. They feel like hypocrites, like slave owners, but they both vow to do everything in their power to see the clones freed. After the war. And the war just keeps, happening, you know? It seems like there’s always somewhere where they and their troops are needed, innocent civilians to save, and they can prioritize civilian lives over the clones’ lives, right? I mean, at least the clones are trained for this. They both care as much as they can for the men they have, but they still lead them to battle, lead them to their deaths, requisition more troops from Kamino with the same forms they requisition more blasters with.
Eventually, as the war drags on and on and on, and their best intentions for the clones are stymied by exhaustion, death, and bureaucracy, both Plo and Aayla realize, independently, that they need to take drastic action if they want to be able to consider themselves Jedi, or even good people. Because they haven’t done right by the clones. Whatever their intentions, they have been complicit in slavery, in child abuse, in murder and torture. Making the clones wait until the end of the war for their freedom is cruel and inhumane, and unless they prioritize freedom and justice for their men now, then they are no better than the slave lords of the outer rim, who sit in their massive palaces with fortunes built on slavery. So, they reach out. They talk to their Commanders. Bly and Wolffe put them in touch with Cody, and with each other. Cody and the other Commanders have been talking, in secret. They, too, have realized that the war isn’t going to end anytime soon, and even if it does, what happens to them?
Cody is reluctant to trust Aayla and Plo, but Bly and Wolffe vouch for them. He asks them, if you are truly willing to help us, you have to realize that this might mean quitting the Jedi Order. This might mean turning against your fellow Jedi. Are you willing to do that? Are you willing to, say, kill Mace Windu, or Depa Billaba, or Ahsoka Tano, if it means our freedom? Aayla and Plo say yes, they are. And they are. This had been one of the toughest choices they’ve had to make in their lives, when it should have been one of the easiest. They are Jedi, and they will fight against injustice and slavery wherever it may be, no matter who is perpetrating it.
So Cody sets them to work. Aayla reaches out to her old master, Quinlan Vos. In this universe, instead of being a racist dickhead, his anti-clone sentiment is born from the fact that he utterly disagrees with the idea of Jedi waging war, and has transformed that into resenting the clones. He’s spent the entire war being literally as far away from it as possible, ignoring the Council as much as he can. Eventually, though, he undergoes a mr. darcy-like transformation, realizes what an asshole he’s been, and when Aayla comes knocking, he’s already been smuggling troopers slated for decomissioning to safe planets.
Plo Koon reaches out to Ahsoka. In the time since she’s left the order, she’s done a lot of growing up. Outside of the stress of constant war, and the influence of the Council and Anakin, she’s done a lot of thinking and also undergone Character Growth, realizing how unfair the clones’ situation is, and how she contributed to it, how she ignored the power differential between them. She jumps at the chance to help. (it does take her a bit to get used to the idea that she’s not a leader here, not a commander- she’s a useful agent, and her input is appreciated, but she and the Jedi with her are not in charge). Ahsoka approaches Rex, he tells her what happened to Fives. Ahsoka does some digging, and uncovers the chips. She takes the info straight to Rex, who, with the other Commanders and the medics, coordinate a massive, secret de-chipping operation under the guise of every trooper needing a vaccine to combat some new disease making the rounds.
Once Cody and the others are fairly sure that the majority of the army has been dechipped, the Commanders make their move, and the entire GAR goes on strike. Every Commander has passed down orders to their captains, and the captains have passed it down to their men, so everyone is briefed on what to do and how to behave. Any troops currently engaged in battle abandon whatever objective they had, fighting only to their extraction point. GAR ships abandon contested space, re-centering around Republic planets and bases. Troopers are ordered to only perform the duties necessary to keep the ships running and keep everyone alive. Food, sanitation, medical, and defense if they are attacked. Many battalions are essentially dead in space, or on whatever planet they were on, because their Jedi leaders won’t relinquish the bridges of their ships, but their troops refuse to fight. So Aayla, Plo, and the other allied Jedi are able to take their troops to these stranded groups, giving them supplies, taking the wounded, helping them defend against separatist forces if they need it.
Cody and the other Commanders have put together a document, and they send two copies. One to the Senate, and one to the Jedi Council. It is a list of grievances, followed by a list of demands.
Needless to say, the Jedi Council are forced into a negotiation pretty damn quick. The Commanders insist that a representative of the Senate, someone with the authority to speak for them, be present too. The clones refuse to send their representatives to Coruscant, because they don’t trust the Jedi Council or the Senate not to execute them. Anakin Skywalker volunteers his ship as a neutral place- sure, the 501st is on strike, but it’s a Jedi ship, so both parties should feel about as equally uncomfortable.
At the negotiations, representing the Clone Troopers: Commander Cody, Commander Wolffe, Commander Bly, and Captain Rex. Plo Koon, Aayla Secura, Quinlan Vos, and Ahsoka Tano are there to, mostly to say what the clones say, but louder and with a Jedi voice, so the council might actually listen. Present on behalf of the Jedi: Yoda, Mace Windu, Obi-Wan Kenobi, Ki-Adi-Mundi, and, ironically enough, Plo Koon, who volunteered when Yoda asked for Council members willing to participate in the negotiations. Present on behalf of the Senate: Senator Bail Organa, Senator Halle Burtoni of Kamino, and Chancellor Palpatine. Anakin is there, too, of course. It’s his ship, after all. Cody starts off by re-listing their grievances, the crimes committed against the Clone Troopers (he’s left the chips off the list- they’re still not 100% sure who’s behind it and don’t want to endanger the troops still chipped). Yoda and Mace try to interrupt him many times, but Cody just keeps talking over them, and Plo Koon keeps going “no let him finish this sounds interesting”.
When Cody finishes, Halle Burtoni erupts into a rant about “traitors” and “defective products”. Senator Organa thinks Cody has a point. A good one. A lot of good ones, actually. Palpatine is quiet, silently calculating how he can turn this to his advantage. Yoda spouts off with a bunch of Jedi platitudes about perspective, the greater good, blah blah blah. Cody just looks at him and says “sir, you’re full of shit.” Before anyone can get on his case for it, Rex stands and starts reading off their demands. Obi-Wan keeps interrupting, with things like “surely, we can negotiate” or “I agree that you and your men have a right to these things, but in war, certain sacrifices must be made” and “can’t this wait until after we defeat the separatists?” Rex tells him to shut the hell up and listen for once in his goddamn life (quote). Obi-Wan turns to Anakin and says “Anakin, I thought you taught your men more respect than that!” but Anakin says “Actually, Master, I agree with Rex.” Before THAT can blow up, Yoda tries to calm things down with “discuss your requests, we must” but Wolffe’s like “Not requests. Demands. We are not here to negotiate, we are here to tell you what you must do if you want to keep your army.” There’s arguing. There’s yelling. Aayla makes an impassioned speech about freedom. Anakin and Ahsoka have a quick hushed aside, in which it takes Anakin about 30 seconds to decide he’s quitting the Order, too. Yoda and Mace ask Plo to back them up, but he just points at Wolffe and goes “my son”. Cody, Rex, Bly, and Wolffe are doing an excellent job of looking like the only professionals in the room.
Eventually, Bail Organa asks everyone to calm down. “Commanders, I hear your grievances, and I understand that you have been treated wrongly. I propose that I introduce a bill in the Senate, to legally grant your demands-by the way, can I have a copy of that list?- We might have to do some arm-twisting to get the votes, but if you and your brothers hold steadfast in your strike, I’m sure it won’t take too long for the Senators to come around- especially those whose planets are close to Separatist activity.” Yoda mumbles something about needing to meditate before taking any action. Bail turns to Palpatine, who hasn’t said a word so far. “What do you think, Chancellor? Such a bill would move through the Senate much faster with your backing.”
Palpatine has been watching the proceedings, and thinking. This could totally work out for him. Anakin and Obi-Wan are on opposite sides of this debate, and he didn’t even have to do anything to drive this wedge between them. Anakin is primed to declare against the Jedi Order. If he plays his ace card soon, the Clone Troopers massacre the Jedi, and, combined with their current strike, is more than enough justification for him to declare them all defective traitors and have them all killed via the chips, leaving Anakin with no one and nothing. Then, it’s a simple matter of unleashing him on the Separatists, having him commit more and more atrocities in the name of victory… unless, of course, Anakin decides to help the clones and participate in Order 66 himself, in which case, his job is done! And he might not even need to kill Padme to do it! At least, not until after the children are born and he can assess whether he wants one of them as an apprentice instead of their father. So Palpatine stands, walks over to Cody, and says, “Commander Cody, the time has come. Execute Order 66.”
And Cody says “Fuck you, Chancellor.” and punches him in the face. In the ensuing shitstorm, a lot of stuff is revealed. Palpatine is a sith lord- the angry Force lightning kind of made it obvious. Anakin has good reflexes, jumping in front of the lightning and absorbing the blast to protect Cody (he’s the most powerful Force-sensitive in a thousand years at least, he’ll be fine). Rex has good aim and good priorities- his pistols are drawn and Palpatine has two smoking holes where his eyes were before Anakin has finished screaming and collapsing dramatically. “Oh my fucking god,” Mace Windu says, realizing that they’ve been living in the pocket of a Sith Lord for a good decade and that he is an idiot. Wolffe is trying to get past Plo Koon, who jumped in front of him the moment Cody punched Palpatine. Aayla and Bly both tried to jump in front of each other (Bly won, because Aayla may be a Jedi but she’s shorter than he is), and Ahsoka, who didn’t get the chance to jump in front of anybody, just goes “yikes”. Obi-Wan, who is currently evaluating all of his life choices and also just how well he really knows his Commander, goes “agreed”.
Anyway Bail gets the bill passed and is elected chancellor, and immediately enters into negotiations with the Separatists (dooku mysteriously vanished, high-tailing it out of there when his master died, and suddenly the separatist forces are much less blood-thirsty and sentient-rights violating when he’s not leading them). Yoda retires to a swamp planet, Mace decides to de-centralize the Jedi Order, re-write a lot of rules and Jedi philosophy, and moves to a new Temple being built on Hoth or something.
The clones are freed, given citizenship, backpay, and reparations, funded mostly by the Senate taxing the shit out of the Banking Clans and the Trade Federation. They objected strenuously, but couldn’t really do much about it with an entire clone army breathing down their necks. There’s a big search for a home for the clones, and a planet that will agree to host them. This is when the clan leaders of the Mandalorian Houses come forward- not the New Mandalorians, but the Mandalorians of the traditional, warrior culture, kicked out of Mandalore by the new government, living as a diaspora all over the galaxy. They say they will claim the Clones as theirs, accept them as their own clan. Their motives are manifold- one, the Clones were trained by Mandalorians, including Jango Fett, and clone culture borrows a lot from the Mandalorians. Secondly, it’ll really piss off Satine Kryze’s government, Thirdly, the promises made to the clones in Organa’s bill could be leveraged into a win-win for the Mandalorian Clans and the Clones. The Clones get their citizenship, and the Mandalorian Clans get recognized as an independent political entity, separate from New Mandalore, and as such, not subject to their laws, and entitled to a Senator of their own, as well as protection and recognition for their citizens spread throughout the Galaxy.
Additionally, many planets offer citizenship programs to the clones, especially those whose populations had been decimated by the war. Governments are desperate for able-bodied people to come in and fill in the economic gap left by the war to stave off economic collapse. The Senate further creates programs to make it easier for clones to gain citizenship on planets that might not be so eager for them to live there, and for clones who are disabled and unable to work. So many clones end up with dual citizenship- Mandalorian Clans, and their home planet of choice.
Many choose to stay in the army- it’s familiar, it’s easier than trying to find a job and pay rent (especially when you’ve never heard of a job, salary, or rent growing up), it’s where their brothers are, and hey, they’re getting paid now. Anakin talks to Rex, and together, they take the 501st to the Outer Rim and wreck shit on the Hutts and their slave empire. After fulfilling his childhood dream of liberating Tattooine, Anakin retires to raise his children with his wife. Wolffe spends a few years traveling the galaxy alone, seeing new places and meeting new people. Eventually he returns to Coruscant, and when he leaves, a newly retired Plo Koon goes with him, and together they see as much of the galaxy as they can. Cody and Rex spend a while helping to settle their vod’e, taking the cadets and babies from Kamino and setting up home bases all over the galaxy, where they are raised by their older brothers. Cody discovers that he loves teaching. Rex finds out that he really likes kids. Eventually, Cody and Rex retire, but they still spend a lot of time with the clone children, and with their brothers. Ahsoka drops by every once in a while. Bail spends his career rooting out corruption and establishing requirements that Republic planets must elect their senators by popular vote. Everyone is reasonably content, oh and also Fives didn’t really die, he was wearing a blaster-proof vest and went into hiding, he rescued Echo and they both live the rest of their lives happily together.