i think there will be some sort of huge disaster towards the end of the clone wars that of course palpatine had known and probably instigated as well. he'll blame the jedi knights, and that's when the hunt begins.
this is pretty logical as it is happening in the world today. PM me if your curious as to what i'm talking about
Sorry boys I had to go to town and I just got back to this conversation. What did I miss? Oh yes the purge of the Jedi. I think Palpatine will somehow get the clone troops to turn against the Jedi(except for Anakin who will be a sith by this time) and think they are doing what is good for the Republic.