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+ Can clone additional heroes and commanders, though, they do take time to develop before they're ready for the battlefield. Perhaps it is time to use the cloning facilities that you used to give the Empire her army to make your own? And, with their human-centric focus, they may decide that having 'aliens' run what gives the Empire most of their soldiers might be a bad idea, and that it might be imperitive to 'remove them'. And the armies you created for it follow them blindy. Kamino and it's rebellion: The Republic we once supported is dead. + Can try to find other Jedi hiding in the galaxy or recruit younglings/padawans on planets you control. Though, you'll need to convince the queen. So, you cannot simply sit on your hands and wait, you need to act know. Yet, perhaps letting you and the other hide on her planet will be a death wish, if the Empire ever learns the truth. Naboo and the Jedi hiding there: Your Order is dead, and would you, if the Queen wasn't so kind. Perhaps they would have fallen to the might of the Empire on way or another." Yet, I do wonder, what would the galaxy would have looked like if, even one of these rebellions, survived. And so, he crushed them, sent the 501rst, Vader's Fist, to crush each and everyone of these. Perhaps a few of them would join him and help his rebellion grow until it was strong enough to challenge the Empire. If he ever revealed what happened on Mustafar to those who had supported the Confederacy during the Clone Wars, that they were secretly in working for the 'dark Lord of the Sith', then. The Kaminoan's and their knowledge of the clones armies would be a dire threat if they were left to their own devices. Jedi? Fools they may be, but, they would never stop trying to destroy all the power he gained, and he himself wouldn't stop till they were wiped out. His own home planet hiding Jedi from him? The Kaminoan's trying to clone their own army? That Geonosian trying to rebuild the Confederacy on the same planet his apprentice slaughtered what remained of the Confederacy leadership of the Clone Wars? These were problems that far outshined a small grouping of rebels spread across the galaxy. In truth, each of these happened, and each time the Emperor learned of these, he became furious. Or, at least that's what the Empire wants you to think.
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'Officially', a certain Geonosian did not try to reform the Confederacy. 'Officially', no Jedi fled to Naboo, with the Queen granting them refuge. "'Officially', there was no clone rebellion on Kamino.