Screencap courtesy of Chrisnu.
The Beginning

All I Need Right Now by Pattie (3K)
Scully considers the gestation of aliens in humans, and how God could let it happen.

Beneath The Surface by Ten (68K)
Explanations for behaviour in the Beginning; just what was going on in Mulder and Scully's minds?

Lifeline by shannono (5K)
Scully tells her side of things following the events of "The Beginning."

Nothing Else Matters by Devin (13K)
From the author: "Your basic fight and make up fic."