Let’s take some time today to imagine a variation on Order 66.When Order 66 declares the Jedi traitors it is believed, without question save for one thing. Each Battalion, each clone is absolutely certain that their Jedi were not traitors (This is, of course, excluding the few Jedi who were like Pong Krell and thought of the Clones as less than human). Their Jedi alone had stayed true (For the purposes of this idea there is a battalion stationed in the temple who consider all of the Jedi in residence as theirs. The Coruscant Guard claimed a number of the Shadows, including Quinlan Vos. Also, by and large the clones consider any Jedi they interact with regularly as ‘theirs’). In addition, through chip related hand waving, the clones believe that only their own battalion have stayed true, all other clones in the GAR have betrayed them and are a danger to the non traitor Jedi.
Frankly Sidious’s words and actions did not dissuade the clones of this. Neither did the actions of the nat borns that supported the new emperor. Instead it convinced the entire GAR that the evil Jedi traitors have somehow taken control of Palpatine. The Nat born officers that claimed their Jedi were also traitors…well those nat borns tended to be the ones treated the clones like meat droids anyway, so it was all too easy to assume they were in league with the Jedi traitors.
Every battalion decided, near simultaneously, that they had to take their Jedi and run. Regroup on some uninhabited world (Somehow none of the battalions managed to pick the same uninhabited world) and any nat born that tried to stop them was killed outright. They could make a plan for saving the former Chancellor and the Republic once they were certain that ‘Their Jedi’ were safe. The Jedi go along with this because 1.) The force is telling them to 2.) They can feel that something is very wrong with their men and 3.)Their men are nearly panic stricken at the thought of their Jedi reaching out to other Jedi.
In the chip-addled minds of the clones they are convinced that their Jedi reaching out to the traitors would be disastrous. Not because they thought their Jedi could be convinced to be a traitor, but because their Jedi was soft hearted and kind and trusting and the traitor Jedi would HURT them, either emotionally or physically.
Anakin Skywalker, in the midst of falling to the dark, still marches on the temple with the 501st. By the time they reach it, the entire thing is empty. Not only that it is stripped bare courtesy of the temple bound battalions who evacuated everything not nailed down (and a few things that were). Even the Force felt different in the empty temple. This was enough to pause Anakin’s fall. It also gave the 501st the chance to convince their general that they need to retreat and regroup on an uninhabited planet with Anakin’s pregnant wife (By getting them both out of the line of fire they prevent Padme’s death and manage to bring Anakin mostly back to the light).
Sidious thinks that with one Order he was going to take control of the GAR and be able to use millions of controlled clones in taking full control of the galaxy. Within 2 days the entire thing, including the Coruscant Guard, vanishes. What’s more his shiny new apprentice has also vanished and not a single one of them is picking up their comms (Communications across the GAR have been shut down to keep their Jedi from being tempted to contact the traitors) and the Force is not nearly as dark as it should be.
This goes on for months, the Jedi trying to carefully coax their battalions to let them reach out to other Jedi. The clones panicking and destroying more communication equipment every time and being in all other ways just to the left of their old selves. No one knows what's going on, least of all the clones, and the war has all but ground to a halt. There is so much trauma on all sides of the conflict that many of the Jedi are legitimately afraid that this was a break from reality on the part of the clones and, not knowing how widespread this was, were concerned that their men would be labeled as defective and killed.
I cannot stress enough that none of the Jedi, save perhaps Anakin Skywalker, knows about Order 66, the chips (though Shaak Ti does know about the chips she did not connect them to the strange behavior of the cadets ), or the ramifications thereof.
Finally, after months, Ahsoka has an idea. She goes to Rex and the other officers (without the urge to kill Ahsoka, Rex did not fight the chip or make the connection to Tup and Fives) and starts asking about who the enemy is, who the traitors are, since they cannot trust the Emperor (who is being controlled by ‘traitors’) or the separatist or even each other really because they came from all different battalions and felt some loyalty to their old comrades. At last she asks if there are any other Jedi/former Jedi that they can reach out to, to start to figure out who to trust. Rex is quiet for a long moment. At last he says that General Kenobi always chooses what is right. Whatever side Kenobi is on is the right one. All the other officers agree.
Ahsoka helps them make plans to track down the 212th. Internally she is a bit horrified because 1) no one being should make up the entirety of another person's moral compass 2) is aware that her grandmaster is, like any other sentient, capable of making the wrong choices and siding with the wrong people 3) she knows for a fact that Rex also knew that and 4)she still has no idea what is wrong with her men.
It takes another few months to track down and make contact with the 212th, a few weeks after that to convince Cody (who very much thinks that they are traitors and should be shot on sight) that they are on General Kenobi's side. At last they find a neutral place to meet and two Jedi meet for the first time since the Order went out.
Obi Wan is ecstatic that Ahsoka is ok. In the intervening months he has learned how to ask questions of the controlled clones where they will answer with information that they do not consciously know (Still never stumbling on the chips or their function because none of the 212th had the correct information). So when he asks Rex if he knows why the Jedi are believed to be traitors, Rex answers with ‘the chips Fives warned us about are active now.’ From this Obi Wan is able to get more information about the chip and convince Cody to have it taken out.
After the removal Cody has a mild to moderate panic attack once he wakes up. Dealing with memories of abducting his general, the death threats he delivered to his younger brother and a Togruta who might as well be his sister, the horrifically uncharitable things he thought and said about any clone not in the 212th. He also wakes up realizing that the Jedi are not traitors and has to reconcile what he would have done when confronted with any of them. I imagine that it is sometime shortly after Cody wakes up that Codywan gets together (I love the idea that they had an understanding that they would explore their relationship after the war, this also neatly skirts the issue of consent while under a mind control chip).
With it confirmed what was going on, the 327th and the 212th began to remove the chips wholesale. There are whole new branches of psychotherapy that are developed as the dechipping continues and Clones begin to realize exactly how kriffed up those chips made their heads. Though the process for dechipping the entirety of the battalions takes months, as soon as the process is nailed down and there are a handful of dechipped clones, they begin to try and track down the other battalions (They find Plo Koon and his Wolffe pack next).
With the rest of the galaxy, the disappearance of the clones and the Jedi has changed both nothing and everything. Palpatine is Emperor in name and function, he has many people in power to back him (Or who would back whomever promised them power). The Jedi do not need to be dead to be scapegoats, just absent. In fact, without the inherent tragedy of the Purge and the march on the temple, they actually make a better scapegoat. What has hurt Palpatine’s regime is the lack of 3 million clones ready to enforce his every command. The nat born military officers that would have supported him are dead, the ones that wouldn’t have chosen to desert with clones and the Jedi. It is too close to the end of the clone wars to use droids. This leaves him entirely without a military at the most vulnerable time of his new regime (When it is between 6 months and 3 years old).
What would have become the Rebellion in the Canon universe is also struggling. Order 66 and the Purge is such a defining moment. It would go on to become the moment of rock bottom for many worlds, the moment where there is nothing left that can be taken away so you might as well fight. Though it may never be pointed at, it was in that moment that many of the Rebellion founders found their courage to fight back, to Rebel, to deny the Empire that the Republic has been for decades. In this universe there is no tragedy of unimaginable proportions, no genocide to spur secret meeting, no rows of faceless white to fight against. Instead we have a tense holding pattern, restrictions that are unenforceable and thus ignored.
Some systems talk about seceding, some just quietly stop showing up. As the months drag on there are more and more empty pods in the imperial senate. More and more systems suddenly stop accepting imperial credits, or abruptly seem to have their own military and won’t take Senate comms. Then entire systems seem to be blockaded from Imperial ships.
Palpatine played his ace in the whole and it was a good one, unveiling his empire. Without the immediate glue of the Clones, that empire began to unravel.
The Jedi and Clones know none of this, creeping between worlds in the outer rim and wild space. Once they discover the planet that the Coruscant temple was evacuated to, it is decided to make this planet their home base, their new home which they call Haven. Once they find where Kamino was evacuated to (thankfully not far), the cadets are moved to Haven. Thankfully it seems that Obi Wan Kenobi remains the only person that every chip-addled mind seems to think would always choose the right side (Everyone, including Obi Wan and the dechipped clones, is both baffled and a little concerned) so Obi Wan can go in with a few dechipped clones to each speak with each Jedi.
By the time they find the 501st, Luke and Leia are just over 2 years old. The forced downtime has given Padme and Anakin the time to actually have several adult and emotional conversations.
Anakin’s march on the temple has highlighted the cliff that he almost stepped off, and without an enemy to beat it becomes very clear that this cliff is something he wants no part of. Something about the combination of 1) Raising children, 2) dealing with clones that even Padme can tell are NOT acting right, 3)No longer being constantly under battle stress and 4) Doing just a little self reflection (assisted by his wife) and reeling that Holy Kriff he was ready to kill kids (He has already done so but this is the difference between manslaughter and first degree murder).
Padme has also realized that she has some very unhealthy mindset she doesn’t want to pass onto the children. There was something about the way the clones agreed with everything that Anakin said that was striking in all the worst ways, for both of them (The chips meant that ‘their Jedi’ could do no wrong).
They are both so glad to see Obi Wan, even more so when he tells them that they have a way to fix/free the clones. The last grip Palpatine had on Anakin’s mind fades when Obi Wan is nothing short of ecstatic for them at the birth of the twins, and is not surprised about their relationship (he is a bit surprised that they are married, and how long, but he just sighs and goes, ‘well I guess no one wins that bet’). The 501st is dechipped, assigned a therapist to deal with the issues caused by the chip (and marching on the Jedi temple), and they are all brought back to Haven.
During this entire process the combined Jedi and Clones are still entirely cut off from the rest of the galaxy. They could not risk being found by the Empire or Sidious and had no idea about who they could trust. They have managed to grow, create, figure it out, or do without everything they could need. It takes ten years to find all of the Clones and Jedi. There is a slowdown in year six that lasts for a year and a half when they start having to ration the fuel for their ships, which led to the more mechanically inclined managing to invent a whole new propulsion system.
After 10 years all of the Clones and Jedi have been found and brought to Haven. With everyone safe it is decided to peek out into the galaxy to find out what is happening.
They poke their heads out into a very different galaxy. The Republic and the Empire have both crumbled under its own weight, without the Jedi or the Clones to prop it up. Instead smaller States, rarely bigger than a system or two, have cropped up across the galaxy. Palpatine was dead, killed by rioters on Coruscant in the final days of the Empire in year 8 (Sith might be able to cause a massive amount of damage, but even they can be overwhelmed by sheer numbers).
In spite of what the Republic Propaganda, and later Empire propaganda, these smaller governments did not immediately throw the galaxy into a lawless free for all. Nor did the lack of Jedi involved cause more suffering that would have happened otherwise.
The residents of Haven decide to adopt something similar, theirs was the only inhabited planet in their system (one of the reasons the Clones chose it) but there were three other habitable planets. Thus the system Tonbrei, named for the Dai Bendu word for completeness and unity, joined the galactic stage and started making trade agreements. Their primary exports were their new propulsion system and teachers for Force Sensitive children.
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