 In the scene with Mulder talking to the Well Manicured Man in the car, he   reveals to Mulder that Samantha, Mulders sister, was abducted by aliens at   the request of her father, William Mulder, so she could be part of the   colonization project, thus ensuring her survival in the colonization of   Earth by the visitors. Also revealed is that when plans went awry, Mulder   was intended, by his father, to seek the truth and reveal what had been   done. 