thanks TheoOdo.

I don't like EU, but this :

Another thing that's very up in the air is the nature of the Clone Wars. In "Dark Empire" Luke finds himself on board a "dungeon ship", which he says is the same kind they used to transport Jedi during the Clone Wars. It's possible to speculate, then, that the Clone Wars may have been a war against the Jedi, involving mass execution and imprisonment of the Jedi. Anakin may have switched sides in this war in order to enjoy the greater power of the Dark Side having been corrupted. At which he point he "helped" hunt down and destroy the Jedi Knights. "Before the Dark Times, before the Empire..."

seems to fit others things I had learn about The OOT's Clone Wars story was the Mandalorian supercommandos (bobba fett was a Mandalorian supercommandos who battled in the clone wars in the OOTP story) hunted the Jedi and that the clones may have been the Supercommandos (a.k.a. Supersoldiers) and Jedi Clones (to aid in hiding the jedi) in The OOT's Clone Wars story.