Behind the Looking Glass by Wendiae

Behind the Looking Glass cover

48,000 Words

Behind the Looking Glass cover

After returning from Philadelphia Scully is unsure of her reaction to Mulder's anger and takes an assignment away from him unintentionally placing herself in grave danger.

This is an all time favourite fic.  I have no idea how Wendiae came up with this case; it's extremely twisted and keeps you on the edge of your seat. The UST is also intense throughout as Mulder roleplays in order to preserve Scully's cover.