This is AU since Mulder isn't in the FBI (for reasons that will become clear). 

M/Sk

 

PART ONE PART TWO
PART THREE PART FOUR
PART FIVE PART SIX
PART SEVEN PART EIGHT  

PART NINE  

PART TEN 
PART ELEVEN  PART TWELVE 
PART THIRTEEN  new PART FOURTEEN  new