This episode follows a pregnant Fauxlivia as she experiences a kidnapping and acceleration of her pregnancy. Meanwhile, her fellow Fringe agents Lincoln Lee and Charlie Francis attempt to locate her as they become distrustful of Walternate.
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The Observer can be seen watching Fauxlivia's apartment before she gets kidnapped. He can also be seen watching Brandon receive the baby's DNA sample in the hospital stairwell.
A folding fan seen in the background in 'Stowaway' foreshadows Fauxlivia giving birth in a Chinatown gift shop in 'Bloodline' that has folding fans hanging from the ceiling.
A small, cartoon bird is seen in Chinatown when Fauxlivia escapes captivity in 'Bloodline'. Broyles sees this same bird in 'Lysergic Acid Diethylamide' during his LSD trip.
In "Bloodline" a pregnant Fauxlivia worried that she was a carrier for VPE, the same disorder that led to her sister's death.