The whole clone rebellions thing? I've been wondering how recently how the two might be merged together in an AU. One would have the whole CIS war starting first, a brutal conflict that exhausts the ranks of the Jedi while Palpatine is pulling the strings. Then around ten years after the war ends, the remaining clone army would "inexplicably" suffer breakouts of insanity and rebel (again engineered by Palpatine akin to order 66). Of course, between the end of the CIS war and the clone wars, Palpatine would've been implmenting the "New Order" to some degree and having an Empire in all but name, also building up a non-clone Army to supplant the old GAR. Perhaps the fight between Palpatine and Windu would be the hollowed-out Jedi council's last-ditch effort to assasinate him rather than an arrest. Shortly before then, Luke and Leia might be born, only for Padme to perish during the Clone rebellion and have her Death pinned on the Jedi by Palpatine, completing Anakin's fall to the Dark Side. (It's a minor detail, but this'd explain Leia's "I remember my mother" comment in ROTJ). Then something like the Mustafar fight would happen.
I shall try to expand on this:
Episode 1:
Set around 45 bby in the decaying Galactic Republic. The Jedi are a reclusive and isolated order after centuries of stagnation. The temple on Coruscant has long been cut off from visitors, and inside the Jedi Council continue their staid examinations of the force and much diminished training efforts. Indeed, among many quarters of the Galaxy, “Jedi” might refer to some kind of Republic Special Agent, in others it’s just a club of people who are dexterous enough to wield a lightsaber, and many other interpretations that often ignore the force entirely. Despite their mixed reputation, the Galactic Senate sees fit to call on them for resolving interplanetary disputes, such as the one occurring on an idyllic outer rim world known as Naboo. The Trade Federation is up to their usual tricks, but this time they’re launching a full-scale occupation of a planet with considerable wealth. Cue the events of TPM up until after Qi-Gon, Obi-Wan, and the Naboo Royal family escape. Their damaged hyperdrive can only handle one more jump. But upon reviewing their options, Master Qi-Gon picks the desolate world of Tatooine. The others are confused, but the old Jedi confides in his Padawan that he has sensed
something of note in the force on the planet, invoking the ancient prophesy of “the chosen one”. Sure enough they head to Mos Espa, following Qi-Gon’s intuition and come upon young Anakin Skywalker ( who Doesn’t build C3PO in this setting), a child with abnormal intuition and reflexes for an uneducated slave. Cue the Pod Race plot with one exception: Shmi Skywalker is also freed, but Qi-Gon tells Anakin that while the Jedi will provide her with an easy life on Coruscant, he cannot visit her again, for a Jedi must let got of prior attachments and avoid building any others beyond the camaraderie of their fellow Jedi as part of the order’s strict code. The Naboo plot proceeds with some differences: the Gungan tribes led by brave general Jar-Jar Binks engage the Battle Droids around Theed to draw them away so Amidala can sneak in, Anakin (with the help of Artoo) Destroys the Droid Control ship over Theed, deactivating the droids protecting Gunray and the other Trade Federation bosses which allows Amidala and the Naboo guards to capture them and forces a ceasefire. Qi-Gon/Obi-wan and Darth Maul fight happens as usual, leaving Obi-wan to train Anakin.
Episode 2:
35 BBY: The Republic is fraying at the seams. A movement dedicated to seceding from the corrupt Coruscant regime is gaining steam, centered mostly in the galactic rim. Pro-unitarian voices like Senator Padme Amidala even face assassination attempts. Anakin is now a Padawan. In addition to being trained by Obi-wan in a more unorthodox manner due to starting the process while he was older than the Jedi code permits, he is also saddled with sky-high expectations due to his apparent status as the “chosen one”. He MUST bring balance to The Force, lift the dark haze that has been clouding the Jedi Council’s ability ponder Galactic affairs, eliminate the Sith, and usher in a new Golden age for the Jedi and the wider galaxy. In addition to these near-fanatical assurances by the council that seem aimed more at themselves, Anakin has been secretly meeting with Padme and the two are forming a bond very much in defiance to the Jedi code. Matters come to a head when Padme and several other senators are in a meeting with the chosen representatives of the secessionist movement that end in an assassination attempt/terrorist attack on the Republic delegation. Said attack is revealed to be part of a wider network that killed many targets and bystanders, including Shmi Skywalker (secretly arranged by Palpatine of course. An outraged Anakin leads the pursuit and
cuts down several of the separatist reps in his anger, prevents their escape by damaging their craft with a lightsaber throw, causing a crash that kills many officials, and collateral damage, as well as directly killing the premier Seperatist rep, and here I must thank
@Skallagrim for the post that inspired this plot point. Of course the Separatists are angered while the pro-republic side views Anakin as giving them their just desserts for fostering the sentiment that incited a dastardly terrorist attack. Obi-wan pursues a lead on one of the killers and we get the whole Kamino arc, where it it turns out that the clones were ordered by wily renegade and long-MIA Master Syfo Dias some 20 years prior following a worse Stark Hyperspace war. The Geonosis plot happens and begun, the clone wars have.
Episode 3:
20 BBY.
The Clone War de jure ended 10 years ago, but the fighting persists as CIS remnants and other groups stirred to action by the war keep fighting. The wily CIS leaders are always on the move and impossible to track. Now we see the consequences of the past 15 years. Coruscant is in a state of martial law and once-active airways are deserted. Palpatine is venerated for leading the Republic through this crisis. As for the Jedi, they have been even more marginalized, if such a thing was possible. They often served on the Galaxies’ worst fronts and took expected losses, and far worse after General Grievous’ raid on Coruscant in 31 BBY. In return their sacrifices received no recognition from Republic propaganda. This is because cultivating fame, glamour and media personality is “against the Jedi way” and “a path to the dark side” so most just went along with it. It is the gratitude of those inhabitants on worlds they helped liberate that the Jedi seek. But the rest of the galaxy has little acknowledgment for them, such that even Republic officers might call the force an “ancient religion”. Anakin has been fighting non-stop on the worst fronts of the clone war and against the worst holdouts (with Palpatine’s careful nudging in the background, of course), and he has given in to his anger more and more. Anakin isn’t even aware that after his last brief visit with Padme a over a year ago, she became pregnant with twins.
Then one day on Coruscant, something unimaginable happens as Clone Troopers begin to turn on their officers and each other. It is the same across the galaxy. The Clone Rebellions have begun. Anakin rushes back to Coruscant after hearing the news. Meanwhile, Master Windu uses the chaos to enact a desperate plan concocted by himself and several other Jedi dissidents: assassinate Chancellor Palpatine, or as they know him, Darth Sidious. But Windu errs by informing Anakin of the plan to try and get his help, not knowing that Anakin has been having his own secret discussions with Palpatine. Additionally, the Clone rebellion on Coruscant has claimed Padme’s life, though Kenobi was able to rescue the twins. Indeed, right after receiving Mace’s message, Palpatine contacts Anakin with security footage of Obi-wan entering Padme’s office…
The results are pretty much what we know. Anakin sides with Palpatine and becomes Darth Vader. Palpatine tells the Senate that the Clone rebellion was the work of the Jedi who also tried to kill him and declares the founding of the New Order. Having planned for the Clone Rebellion, he already had a large non-clone component of the GAR assembled over the preceding 15 years and ready to fight. Loyal clones will still be part of the military, but the stigma of “clone madness” will leave clone experiments firmly under the onus of Palpatine and a few isolated renegades. Now the Empire will set about crushing the CIS remnants and clones with the goal of bringing peace to tve galaxy. A few renegade clones even side with the CIS hodouts, the discarded puppets of Palpatine forced to work together for survival. The Jedi Temple purge happens as usual and Anakin is then sent to Mustafar by Emperor Palpatine to “take care” of the Speratist leadeship. Cue the Mustafar fight and Anakin’s transformation to Vader minus that embarrassing “NOOOOO!” Then we’re all set for the OT.