Outwardly William Mulder seems cold and aloof to his son when he calls him home to see a stranger who claims to be his daughter. We later learn that there is a reason for this. He was terrified that Mulder would find out about his secret involvement with The Smoking Man. In a conversation with the Smoking Man, they appear to be on first name basis. Eventually he finally tries to admit in what he had done only to be shot by Alex Krycek, possibly under orders from the Smoking Man. His last words were a plea of forgiveness to his son. We soon learn that Samantha Mulder was taken to make sure that her father kept quiet about the cover-up. He was forced to make the choice of which one was to be taken, it was decision that he had to live with for the rest of his life.