He ordered his battle droids to begin occupying systems that had now been left defenseless. Instead of being met with fear and terror, as they usually were, the Republic people seemed to almost welcome the invasion. The battalions of droids were not resisted in any way shape or form. Even when capital cities were overtaken by swarms of the droids, no one really panicked. Droids won't revolt, the people argued. They're programmed, they wouldn't turn on their leaders, their beloved generals like the clones did.
When the clones were redeployed, chip-free and extremely traumatized by the possibility that Order 66 might have been a mistake, that they betrayed their Jedi for nothing, they realized that the terror was just beginning. It was their presence that was met with protesting and resistance. People swarmed to the streets, even to the battlefield, shouting for the clone troopers to go back where they came from. They created meat shields around the droids, creating signs and blocking their paths into their cities. The protests began to spread until hundreds of senators reported that their people were refusing the protection of the clones.
Some of them had to bow out immediately. They had elections coming up soon, and if the chaos remained for any longer, they would lose their seat in their system's government. The Republic pulled the clone troopers from those systems, much to the rejoicing of their people. Some of them already had battle droids there, so when the Separatists began reaching out to them, alerting the governments that a truce was able to be made if they wanted to be free of occupation, some of them joined right up. The droids were already here anyway.
The systems that remained loyal to the Republic were almost disgusted by the betrayal of these systems, but when those senators did not do the same, the protests began turning into riots. Civilians marched onto the government campuses by the thousands, demanding that their leaders get rid of the clones that roamed their planet. Of course, most of the time, it was the clones who were guarding these buildings, which only escalated the tensions. More Senators began leaving the Republic, tanking the economy and the Republic's hopes at winning the Clone War.
Just when it was thought that it couldn't get any worse, when entire systems were on the verge of civil war and the Republic Senate was about ready to make a move, Dooku pressed the magic button that sealed the fate of the Republic. Broadcasting on all frequencies, he declared to the entire galaxy that the Confederacy of Independent Systems was forming itself into an Empire, one that sought to unite the whole galaxy under one banner. Under this new Empire, Dooku promised that any clone forces identified in Imperial systems would be hunted down and executed for treason against the late Chancellor Kanai and the Jedi Order.
No one even questioned why a Sith Lord would want to avenge the Jedi. All the people heard was 'clones would be hunted down and executed' and they were in. Riots in Republic systems went from tense and uncivilized to downright violent. Citizens with weapons brought them to their protests, and the people took it upon themselves to carry out the Empire's promise. It didn't matter if their government didn't join with the Empire, because the people were already loyal to it. Clones began dropping like flies all across the galaxy. Protesters began screaming things like "Justice for the Jedi!" and "All hail our glorious Empire!" If what remained of the Republic Senate hadn't gotten the message by then, they got it now. The Republic broke apart, dissipating into nothing in a matter of days.
Kamino called for the full retreat of the clones, and it was up to them to tell them that the Republic had been disbanded and that the Clone War indeed was effectively over. Everyone was glad to get out of the riots, even if it meant that their entire purpose had been served. They didn't want to be among those who had been killed by the new Imperial citizens.
Instead, days later, Dooku launched a full invasion of Kamino. A few agents were sent in to retrieve specific data from the Kaminoin database, but other than that, the droids were ordered to obliterate the planet. Yes, a few clones managed to escape in the midst of the chaos, but the majority of them were destroyed. Over a decade and a half of work went up in flames, only to be quenched by the raging sea underneath them as the supports went down and the buildings collapsed. All life on Kamino was lost beneath the crashing waves, to be ridiculed and later forgotten.

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Back in the Game (COMPLETE)
ActionThe Clone War has resumed after its brief pause due to the fall of Chancellor Palpatine, who has been revealed to be Darth Sideous. Chancellor Kayla Kanai leads the Republic, and Darth Tyrannus has seized control of the Separatists. The war is now a...
9.17.4
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