This is definitely one of those episodes you shouldn’t watch after a few beers. It’s pretty complex, and require one more pass at it just to be sure. However it seems confirmed that this kid Emily is indeed Scully’s child, Mulder has a hard time proving it to the judge however when he tells the story of Scully’s abduction and possible theft of ovaries, then used to make a child.
It seems that Emily starts to become ill when she’s taken into care and removed from the help of her old doctor, a man who works for a pharmaceutical company. When performing tests on Emily, Mulder and Scully notice a green sis on the back of her neck, when punctured – it emits a poisonous substance that seem to burn peoples eyes out – sound family? (strange Mexican episode). In fact, Mulder cautions people when approaching her based on previous experience. With not much else to go on, Mulder tries to beat the cure out of the doctor – only to find out he’s being lead around by bounty hunters! One of which takes on the form of the detective to deter him and make him loose his way.
On searching around the lab he finds a small green jar with a tiny baby inside, still alive and kicking. All in all, I’m not quite sure what to make of this episode. I know it ties in with the previous conspiracies of alien\human hybrids (the green blood), and shape shifting alien bounty hunters, but can’t figure out what it has to do with Emily and Scully.
Still the fact remains that Emily dies of her illnesses and no body is found – expect the gold cross which Scully gave away.