Question: is mulder the father of scully's baby?
Answer: But as viewers learned in the season 11 premiere, William was not biologically Mulder's son — he was CSM's, who drugged and medically impregnated an unwilling Scully. ... As Mulder grieved the loss of his son and what his life meant without his fatherhood, Scully told him he was still a father: she was pregnant.