It must have started when Sloane has gotten hold of all 47 Rambaldi devices & assemble it together. That's why he was crazy enough to convince Jack to re-kindle their partnership, among that, Sydney will never be a pawn in this deadly game again !! Second, after the catfight between Syd & Freclipica(Allison), Sloane took Syd put in a time machine built from Rambadli parts & sent her two years into the future, this would explains why that Vaughn believe that Syd was dead, thus being married to someone else. Of course, that's my theory, I could be wrong, but who knows. Finally, if you remember Page 47 from the 1st season showing Sydney as the descendant of the Prophecy & Irina must discovered something in those atrifacts which would meant Syd was chosen to stop whatever Sloane was going to do by finding a way back into her own time (2003). Because Syd's hair should've been longer than it is now & the scar on her lower abdomen was there recently. That's all I want to tell you, if you have ideas you like to add, feel free & reply when get the chance.