The main-plotline that runs through the series is of a massive cover-up involving as yet unknown forces (possibly governmental) who have made contact with extra-terrestials and are co-operating in abductions, experiments and various unsavoury deeds. Agents Mulder and Scully have found themselves through their investigations knowing a lot more than the men-in-black would wish them to know.

They are not alone in their quest for the truth, a number of shadowy characters have come to their aid and one in particular has paid the ultimate price. A number of times, they have come tantilisingly close to their goal, only to be thwarted by enemies and even their allies, as yet they have collected no tangible evidence of the existance of this secret cabal.