Speculating on Stargate Atlantis Season 3

So I've been fighting a cold the past few days, one of those where the fever makes your eyes hurt too much to look at a computer screen or television.  So I fired up the DVDs I've burned of SGA season 3 up through 'Progeny' and dozed for most of the day yesterday.   So as I dozed to the comforting tones of John, Rodney, Carson, & co, I started to think about what lies ahead--especially the next episodes that lead up to the half-season cliff-hanger.

( Spoilers and Speculation for SGA Season 3... )