<P> In later seasons , it is revealed that he is a member of a group known as the Syndicate , a shadowy organization within the United States government . The episode `` Two Fathers '' reveals his birthname or alias as C.G.B. Spender , and that he was formerly married to Cassandra Spender , with whom he had a son , Jeffrey Spender . He recruits FBI Special Agent Diana Fowley to be a subordinate of his because she has a close relationship with Mulder . In `` One Son '' , Jeffrey finds out that his father , the Smoking Man , forced his mother Cassandra to undergo medical treatments that led to several nervous breakdowns during his childhood years . When the Smoking Man finds out , he seemingly kills Jeffrey . Knowing of the colonization plan , the Alien rebels return to Earth to try to persuade the Syndicate to join their side against their war with the Colonists . Not believing in the strength of the Alien rebels , the Syndicate members meet at El Rico Air Base to be transported to a spaceship to survive the colonization . However , the rebels appear instead of the Colonists and kill all remaining chief members of the Syndicate . Together with Fowley , the Smoking Man escapes the destruction of the Syndicate . Later in the sixth season , there is more evidence that suggested that the Smoking Man is Mulder 's biological father . Eventually in `` The Sixth Extinction II : Amor Fati '' , Fowley comes in disagreement with him . Because of his plans to kill Mulder , Fowley helps Scully in her investigation to locate Mulder , which leads to her death . After the destruction of the Syndicate , the Smoking Man starts to operate as he wishes . However , his cancer resurfaces , and he begins using a wheelchair and has a tracheotomy . In the end , Alex Krycek and Marita Covarrubias betray him in the episode `` Requiem '' , throwing him down a flight of stairs , where they presume him to be dead . </P>
when did we find out the smoking man was mulder 's father
Later in the sixth season