As I mentioned in the last post on the show, it seems the main baddy for the series is this "Clairvoyant." And with a name like that, the natural reaction is to assume that he/she is psychic or some sort of spooky being or something.
But all the stuff that has been attributed to the Clairvoyant, could easily have been managed by a mole or evil-doer within the S.H.I.E.L.D. organization. There hasn't been any big reaches by this entity, it's all been basically a knowledge of everything that's going on with the team and people who have some contact with S.H.I.E.L.D.
I haven't seen this theory broached on any of the sites where I check on the show (not that I hit a great ton of them) so either I'm way ahead of the curve, or completely off the tracks on this.