i think syd was captured by someone maybe sark and irina, and had been psychologically reconditioned somewhat and had been missing for that long in custody of sloane or irina (and does ne1 think that prophecy was really about syd?)
I definitely think that the Prophecy is about Syd because of what Irina told her on the roof.
But as for the phsycological reconditioning- I'm not really sure. I don't think there was enough about her personality to show-- though she seemed to remember her CIA I.D. number and so forth.
if it is a choice between irina and sark, it would have to be irina because sark was captured by the CIA. i wonder what they're going to do with him next season...
i still think that rambaldis advice was time travel thing that when set off setnt prophecy child which he thot was himself to a certain time...he accidentaly sent syd