I go back and forth sometimes, wondering whether the Emily arc or the William arc is more cruel to Scully. And there are times when I think it has to be Emily, because Scully had no choices anywhere along the line. And as a fellow control freak, I find that so, so horrifying.

That is an excellent point. But I always assumed that Scully gave William up for adoption because she was forced to do so. She felt like she had no choice. I also assumed that losing a child you had known and loved passionately was worse than losing a child you had barely met, even though the circumstances of her death couldn't have been more horrifying. I believe that Scully could eventually become reconciled to the loss of Emily, the miracle that wasn't meant to be. I don't believe she could ever get over losing William.

After I have reread the story, I may ask for your take on the WTF moments.