I'm thinking this whole thing has something to do with Rambaldi. He's going to try to get together all the missing pieces and keep everything for himself. What if Sloane *is* Rambaldi?! Nah, that would be too weird.
But I guess we know now why he was always so protective of Sydney and Jack. He didn't care about them personally, he just wanted to keep them safe so they could do his work for him! What an evil bastard!