Figured the only way they could even do a third season would be to have Brody on the run through the whole thing. I originally figured he'd find out about the plot to kill him and disappear, but after the spook with the heart-o-gold decided he wasn't a bad guy in the finale I figured I'd end up being off. The terrorists releasing the tape of Brody though was a shock, though the CIA ofcourse knows the video came from long before... I'm guessing the assassin having a change of heart was to make the chase that much more "emotional" next season as he is likely going to be the one hunting down Brody.