i think it was walternate's plan all along for fauxlivia to get pregnant. when peter left the other side to come back here, walternate said he'd accounted for peter's other relationships, but underestimated peter's relationship with olivia. and going back and watching "do shapeshifter's dream of electric sheep?", we can see tj newton constantly egging fauxlivia on.
THOMAS NEWTON: I don't know what your mission is, Bolivia, and you've made it very clear that it's none of my concern. Whatever it is, I imagine it requires you to gain Peter Bishop's complete trust.
BOLIVIA DUNHAM: What makes you think that I don't already have it?
THOMAS NEWTON: Well, maybe it's because I'm looking in from the outside, but I'm willing to wager that somewhere, deep inside his brain, Peter Bishop senses that something is not quite right with you, that something has changed, that you're not his Olivia.
BOLIVIA DUNHAM: Okay, you need to remember who you're talking to.
THOMAS NEWTON: You're in over your head. You're not fully committed to this task, and because of that, you will fail. (hangs-up)
later, at the end of the episode:
Newton: "[You're very good] at continuing to try to convince yourself that you don't care. But you do care, don't you? Every night when your head hits the pillow, in the last moments before you go to sleep, your emotions betray you, and you question your ability to pull this off. Words like, integrity, self-respect - they haunt you. They form a line that you're unwilling to cross and that will lead to your undoing. But I suppose that's not my problem anymore."
newton was always working for walternate long before fauxlivia came over here, so i think he was meant to convince her to take her and peter's relationship to the next level. she clearly is frightened of her feelings for peter and doesn't want to jeopardize her self respect or relationship with frank back home, but newton convinces her that she must "cross the line" in order to complete her mission successfully.
and as far as the blood sample from baby bishop, there is an official photo from fox going around that shows walternate taking the card directly from the doctor, not from brandonate, that was not shown in the episode. im not sure if this should be taken as cannon, but if it is, then i think brandonate is going behind walternate's back and giving the baby cortexiphan, the sinister bastard. and it also follows reason that baby bishop shouldn't be able to operate the doomsday device, as it was made for peter alone (by the first people, not walternate). if it has to do with peter's dna, walternate himself could operate the machine, and there would be no need for babies at all.
apologies for this insanely long post!
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