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Anacaona
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You solved the X-Files! Great analysis!
I do think you are missing a key part that shows that this is not a downer ending for humanity on the making: God.
Let me explain my personal theory of the rest. The aliens met God and he instructed them to give us those holy books and mix their DNA with ours before they left

Carter has lied a lot of protect plot points so I don't take those declarations in account too much. He does write things last minute to avoid leaking but that is kind of standard specially since the Internet was already starting with the leaks and spoilers ruining the experience and Carter is very secretive. I'm sure

I can see why you read the show this way. I really don't see it that way though. The show is based on UFO lore that deals with similar issues on abduction and pregnancy and human/alien hybrids. I also think the word barren is a better choice than the proper medical term is a good reminder that this is a personal loss

I give more credit to Chris than most fans but I do think his abduction will play a role and it will be mentioned or at least once the show ends for real we will have a pretty good idea of what happened and why it was important.
My personal theory is that Cancer Man send him to the ship to get abducted because he knew

Well the multiple personalities lady said that they always get separated and that they come back to learn their lessons. I read it this two are supposed to fall in love but it never works Scully and Mulder always end up spending a lifetime bonded, so that is the lesson they needed to learn that is why she was meant to

You mean that kids are like adults different from each other??!!! I'm shocked! :p

Likewise *waves* and you were right! At least I'm sure we will see Ma Scully ghost to help save the day for sure. All other parents had appeared after dying she cannot be less. In fact I think she changing her will to allow herself to die might had been because she found out she will be more useful in the other side,

If you ask me this was the plan all along. Is too much of a coincidence that Mulder found out what happened to Samantha a few episodes before Scully announces her pregnancy.