But you know, I think the episode would have been better if they skipped the Atavus altogether and just had Sandoval be the villain in season 5. He's got the mothership and absolutely nothing left to lose. At that point he could probably try a world domination plot all by himself and stand a decent chance of success.
Kind of makes you wonder why Sandoval never tried anything in the months between season 4 and 5. After all, he's in command of the Mothership, which still has a full complement of Volunteers, including the shock troops which served as Zo'or's personal guard. Yet all he does is shoot shuttles which approach? I know he was scarred and disfigured, but come on.
Like I said earlier in the thread, Sandoval is only really a threat when he has alien masters whipping him.