Originally Posted by TK-8252
By the time of RotS the ARC Troopers had already been removed from combat and sent back to Kamino to pass on Jango's knowledge to the new Star Corps Clone Commanders.
The Republic Commandos didn't have much of a role in Order 66, since it's mainly for the clones who were assigned to a Jedi General, in which the commandos were not. But they probably recieved word that the time had come, and if they had came across a Jedi they'd kill them without hesitation (they had their independence modified same as the Clone Troopers, after all).
Pretty lame if you ask me. I think this is a convenient excuse to let the "heroic" troopers that people got to play as in games and idolize up until now go "untainted" by the actions of the Empire. I mean, who wants to see their heroes murder the Jedi so the bad guys take over?
It's sort of like how they gave Boba Fett this "sense of honor" and make him help out the good guys sometimes rather than just a greedy egomaniac who enjoys killing (like any good bounty hunter/mercenary!).
Ah well, if I were in charge of the EU...!