The finale of Season 11 of The X-Files has a few things to tell us if we look at the types the characters represent:
Cigarette-Smoking Man = the will to power (his stated goal is to wipe out most of mankind in a manufactured plague and remake it in his own image rather than God’s)
Mulder = faith
Scully = scientific rationalism
William, whom the show’s mythology revolves around this season, is not Mulder and Scully’s son, but rather the son of the CSM and Scully using ‘alien technology’. Thus, he represents the union of the will to power and scientific rationalism. And what is the result? A ‘superman’, a monster, the new advanced race of men that the satanic Elite want to bring into the world (more on that another day).
On one level, then, William is a warning: Do not let science serve evil men.
On another level, however, there is a dim Christlike parallel in William. His father, CSM, views him as a savior of the human race. That is why he brought him into the world to begin with. Most of ‘MSIV’ is William’s ‘Gethsemane’, his pleading with anyone and everyone to save him from his fate as ‘redeemer’ that his father has chosen for him. But by the end, he willingly accepts death at the hands of his own father (a very post-Schism, Western European kind of salvation story), though this is done deceitfully, and thus saves the world from the culling and repopulation for which he was the key.
Later, he is shown to ‘resurrect’ from his watery grave. This latter bit is William’s katabasis, his trip to the underworld that purges him of his sins and troubles. Now that everyone considers him dead, he can live in peace. He has obtained ‘Heaven’.
It is also revealed at the very end that Scully is carrying Mulder’s child. Both beyond their prime child-bearing years, Mulder and Scully have become a modern embodiment of Abraham and Sarah, miraculously bearing the new child of promise. In this child, we have the symbol of the reconciliation of the dialectic of faith (Mulder) and rationalism (Scully), belief and unbelief, heart and mind, that was unleashed upon the West when she left the Orthodox Church in the 11th hundredyear, and the conflict between which has been the driving force of The X-Files for all these years. Mr Carter seems to be offering Westerners hope that such a reconciliation will occur one day.
But they needn’t wait for any new work of man to bring this about. All that is required is the re-baptism of the West into the Orthodox Church, which was her original Faith and the Faith of the Apostles, and in which heart and mind are not in conflict but in harmony with one another by the Grace of the Holy Ghost.
Gather you mind and compel it to enter into your heart and remain there. When your mind is firmly in your heart, it must not remain empty, but must incessantly make the prayer: 'Lord Jesus Christ, Son of God, have mercy on me!' And it must never fall silent. Through this the whole string of the virtues: love, joy, peace and the others, will make their abode in you, by which, then, every request of yours to God will be fulfilled.
--St Nikephoros the Hesychast, entry for 4 May, http://www.abbamoses.com/months/may.html
Holy Ælfred the Great, King of England, South Patron, pray for us sinners at the Souð, unworthy though we are!
Anathema to the Union!