Its really convuled the back history of the program so heres what happened to Mulder.
Basically at the end of the previous series Mulder and Scully went back to where the first episode was and mulder was adbucted by the aliens from that episode. Doggett was brought in to find mulder and having found a double (alien) of which promply escaped, Doggett decided to join the X-files as he thought it probbly is the only way to find him, much to the disdain of his superiors. Now Scully is the beliver having seen Mulder abducted and Doggett the sceptic.
And why because David Duchovney wanted to leave
Basically at the end of the previous series Mulder and Scully went back to where the first episode was and mulder was adbucted by the aliens from that episode. Doggett was brought in to find mulder and having found a double (alien) of which promply escaped, Doggett decided to join the X-files as he thought it probbly is the only way to find him, much to the disdain of his superiors. Now Scully is the beliver having seen Mulder abducted and Doggett the sceptic.
And why because David Duchovney wanted to leave