So at the beginning of the clone wars the senate allows the Jedi to lead the clone army since they defended the republic and were trusted
As the war nears the end, the Jedi start using the army to take over planets that aren’t military targets but are of religious importance (like sith temples). Public thinks they are warmongers for going after non strategic targets.
Anyways order 66 happens, and Darth Sidious orders the clone army and its fleet to attack Coruscant and invade the planet. So far in the war the core of the republic haven’t even seen a clone trooper, since the thought of mercenaries occupying the streets would be distasteful to them.
So the clones attack but are successfully thwarted by palpatines republic garrison forces. This attack is seen as a military coup. And even though no one saw a Jedi in the fight, they assume they were all just cowards hiding on their Jedi cruisers above orbit.
The Jedi traitors have to be dealt with, and Anakin Skywalker, a Jedi defector leads the hunt, and the rest are rounded up and defeated. Except for Obi wan, his former master, who beats him in a duel on Mustafar.
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