I actually think, in a way (though this will obviously serve as a difference in opinion from the get-go), that this fic paints Mulder and Scully as more real than ever; they are out there in the universe (the same one we occupy and function in), and better yet, they know what we're up to. And they are of course, in turns, amused, very unamused, and exhausted by us. Considering the world of fanfic, I can't find this anything but clever.
I say this as someone who absolutely must see, even believe, the characters to be real in order to write them, and even to read them - but this is a state of mind, not a constant state of being, if that makes sense. It's something I can slip out of if, say, I end up finding myself reading a badfic, because Mulder and Scully, in my mind, really shouldn't have to exist in such universes. Good fic, however, makes them real again, and so on.
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I say this as someone who absolutely must see, even believe, the characters to be real in order to write them, and even to read them - but this is a state of mind, not a constant state of being, if that makes sense. It's something I can slip out of if, say, I end up finding myself reading a badfic, because Mulder and Scully, in my mind, really shouldn't have to exist in such universes. Good fic, however, makes them real again, and so on.