Revenge
Spoilers: All Season One, Two and Three
Disclaimer: I don't own Fringe, if I did...well Olivia would still be with Peter.
They think the substitute memories replace her own, they think she doesn't remember who she really is. They don't think she'll try to get back...
What they don't know is that she's buying time.
That she's trying to get near a Fringe event to set off an ability...
That she's trying to kill him...