I'm surprised no one else has mentioned this yet, so I might just be crazy...
Jill may very well BE Fulcrum, and been in their pocket for a VERY long time... after all, it does seem kind of suspicious that she would have been close to Chuck, who Stanford had their eye on for the CIA before Bryce defused that situation. Suddenly, Bryce is the CIA's golden child, and Jill 'mysteriously' decided to dump Chuck for Bryce, who then later made claims as BEING the Intersect. Later, Chuck's not-very-subtle shenanigans might just be tipping off Fulcrum to Chuck's being the real Intersect, then finagling a trumped up network issue at the science conference requiring the skills of one Chuck Bartowski, Nerd Herder and part time secret agent... and the rest goes from there...
I could just be crazy, though...