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X-files Question
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For more on marking an answer as the "Best Answer", please visit our FAQ.in the beginning of an episode in season 7 called 'all things' you see scully getting dressed in mulders bathroom with him asleep (minus his shirt!) behind her. i think they intended to point us in a specific directionso viewers would jump to our own obvious conclusions about that why shes there tehee. there are more pointers like this after william is born i just cant remember them exactly right now. im now pretty sure that mulder is the father and they did get down and dirty! or maybe skinner is the father ;)
Mulder is the father - after undergoing fertility treatment, in which mulder provides the sperm, scully fails to become pregnant. When the last chance fails she returns home to mulder who comforts her and they end up spending the night together, the miracle is the fact that scully becomes pregnant naturally even though she is baron. The baby is born with E.T powers, but is not an alien as such, which is why she has him adopted to protect him. I suspect that one day this story line will be followed up. But Mulder is the father.