I wonder if Jack Bristow isn't a triple agent. At one point during the first two seasons it seems to me that Sydney is going to be shown that she doesn't work for the CIA, but for her mother and father. Remember Rambaldi's prophecy. I could be wrong, still that would be something! Jack Bristow is a very good CIA agent. But Sydney is better. She didn't get the virus even though she was way more exposed than Vaughn. I am beginning to think Will is The Man.
Jack's ruse with the explosives to show Sydney that her mother is a liar...that was so badly done. Jack must have known that.
But maybe the whole idea is to win Sydney to her mother.