In the third season finale titled Resurrection it is implied that Sydney is essentially Jack's pet project - most likely concerning Rambaldi and his prophecies. When she is reading all the secret files about her life, her father enters the room and says: "You were never meant to find those."
Later it was very akwardly retconned so that the files only stated that Jack murdered Irina. Stupid move since it would have made much sense if Jack would have been revealed to be the man behind The Covenant and a far better follower of The Order than Arvin Sloane ever was. Also I can't imagine a better nemesis for Sydney than her own father.
Was the fourth season a pinnacle of network interference or just a really dumb move by Abrams and the writers?