Question: when did we find out the smoking man was mulder's father?
Answer: Later in the sixth season, in the sixth season

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