After the two-parter 6X11: Two Fathers / 6X12: One Son that had a feeling of series finale, the show must go on! These are the first post-Syndicate episodes, and the change in tone of the shows is evident: XF take a more personal, introspective turn. Storylines build on science-fiction bases to develop themes of spiritualism, heroism, and love. This is the beginning of character arcs leading our agents to 7X22: Requiem, at a time when it was believed season 7 would be the final one. The final countdown has begun, and this is adressed at the beginning: Scully: "What more could you possibly hope to do or to find?" Mulder: "My sister." As nearly all mythology episodes, these were developed by Spotnitz & Carter. Originally, this would have been a four-parter (!), with 3 episodes closing season 6 and a conclusion opening season 7; then production issues brought this down to a two-parter, a season finale and a season opener; eventually, Duchovny's input in the story expanded the season 7 opener into two episodes. The final result is 3 episodes that have a strong opening (Scully's reflections in Biogenesis), a weak middle part (the slow-paced The Sixth Extinction), and a conclusion that stands aside from the rest (Mulder's dreams in Amor Fati). Characters and threads are brought back up from past seasons, and no less than three recurring characters (Fowley-Kritschgau-Hosteen) die by the end! The X-Files writers are accused of making it up as they go along, but wow! what a result!

The Ship: the origin of Mankind, the origin of life

What was already hinted at with the findings with Gibson Praise (5X20: The End, 6X01: The Beginning) is developed and confirmed here: the aliens created Man! They are God. They are the beginning, and with the colonization they are the end. We are only tools that they created, hardly nothing more than self-conscious vessels for them to use when they return. Barnes says "There is no God", which sounds a lot like Nietzsche's "God is dead" (the same Nietzsche as "Amor Fati"). Ideas of an alien origin of Man or of archaelological finds relating to alien visitors is fertile ground for science fiction stories and various cults. To name just a few: "Quatermass and the Pit" (1968) of the seminal "Quatermass" british series, where excavations in the London Underground reveal ships and bodies and release a curse; the works of Swiss Erich Von Däniken, notably his seminal book "Chariots of the Gods?" (1968), which documented 'proof' of alien visitors ('paleocontact' and 'ancient astronaut' hypotheses) in ancient cultures; the church of Raël, which believes we were genetically engineered by aliens; the church of Scientology, which believes our souls come from aliens caught in ancient galactic battles; and so on...

Mulder: "it would mean that our progenitors were alien, that our genesis was alien, that we're here because of them, that they put us here. [...] All the mysteries of science, everything we can't understand or won't explain, every human behaviorism, cosmology, psychology, everything in the X-Files, it all owes to them. It's from them." Just as Gibson Praise was "the key to everything in the X-Files" because of him being biological evidence to Man's paranormal abilities, the fact that 'we' come from 'them' would explain a lot, and can even be tied with non-mytharc episodes (for the fun of it!): channeling (1X12: Beyond the Sea), healing (1X17: Miracle Man), genetic memory (2X12: Aubrey), shapeshifting (4X20: Small Potatoes)...

On the surfaced ship, Scully finds engraved a series of words that she transcribes as the familiar four nucleotides that make up every terrestrial being's DNA: adenine, guanine, cytosine, thymine ('adenine' is even misspelt as 'ademine', you nasty aliens!). Albert Hosteen was about to make similar discoveries ("another section [...] seemed to be random letters"). Scully: "On the top surface of the craft I'm finding words describing human genetics." "24 panels, one for each human chromosome. A map of their makeup. Maybe a map of our entire genetic makeup. A complete human genome." I won't go into the odds of billions-years-old aliens calling and writing these four molecules with the same name and spelling as in modern-day English. I won't go into the impossibility of an entire human genome fitting the surface of some 30-metre wide ship either (there's not even enough place to write the genome of a bacteria -- human DNA covers 750 megabytes of data)... Still, humans have their DNA organized in 24 chromosomes (22 autosomes, paired in humans, and 2 sex (XX or XY) chromosomes, for a total of 46). The ship carries on it the blueprints for making a human being! The goal of this very ancient ship was creating Man.

Although emphasis is put on Man, the overall picture that is presented to us is that the aliens not only created the human species -- though this seems to be the ultimate goal -- but life on Earth itself. Scully's questions on the origin of life throughout Biogenesis are answered by her findings: "all [humans] descended from that original single cell, that first spark of life. But for all our knowledge, what no one can say for certain is what or who ignited that original spark". Barnes states that the ship "is only what we call 'God', what we call 'creation', the spark that ignited the fire that cooked the old primordial soup, made animate from inanimate, made us". The 'primordial soup' or 'primeval soup' is a term commonly used to describe the ancient seas or water bodies of Earth some 3 to 4 billion years ago, where organic molecules slowly formed and 'somehow' developed into life. DNA of alien origin exists in human DNA (Fight the Future and The Beginning) and by extension in all living beings on Earth (it may not look like it, but the DNA of a human and of a tree is amazingly similar; humans and apes share 98.8% common DNA).

So the ship came on Earth and created life on Earth using alien DNA and the primordial soup. Evolution brought changes, but the alien DNA remained until today. Perticularly in the human lineage, the 'junk DNA' that would be used as an 'external information tank' for the creation of a grey was conservated (see 6X01: The Beginning).

Life resulting from inanimate matter through processes that are not yet fully understood is called abiogenesis -- creation from something not living. This ship effectively brought life to an inanimate Earth: this is biogenesis -- creation from something living. This ties in with the concept of panspermia, talked about in 4X09: Tunguska -- the fertilization of many worlds from one wandering source. Mulder and Scully describe it here: "Panspermia. It's the belief that life originated [...] elsewhere in this universe. [...] It's the idea that Mars or other planets were habitable long before Earth and that cosmic collisions on these planets blasted microbes into our solar system, some of which landed and flourished here." This belief is often fueled by findings such as carbon compounds or organic molecules (not life) on asteroids, or what is believed to be fossilised bacteria on Martian rocks (Mulder: "In 1996, a rock from Mars was found in Antarctica"). "It's just a theory", but not as improbable as it sounds. And again, even if the origin of life on Earth is from biogenesis, abiogenesis must have occured somewhere, sometime, somehow...

Scully also talks about the mass extinctions that have plagued life on Earth. Many extinction events have happened in the past and it's very difficult to estimate each one's importance based on such a partial record as fossilised remains, but generally five great events are categorized as mass extinctions in the last few hundred million years: 500, 450, 350, 250 and 65 million years ago. Each time, groups of species disappeared, life survived and evolved into something new. What Scully says in the teaser is scientifically correct (although nobody's perfect: she says "Reptiles emerging independent of the sea only to be killed off. Then dinosaurs, struggling to life along with the first birds, fish, and flowering plants".

Even though birds and flowering plants developed alongside dinosaurs, fish predate the dinosaurs by a couple of million years: indeed fish evolved to amphibians, which led to reptiles (and dinosaurs (and then birds)). Further nitpicking: Scully says repeatedly "matter and gas" whereas gas is matter! I guess she meant 'matter and energy'...). There are plenty of theories for the reasons behind these extinctions, but the reasons for what is fastly growing into the sixth extinction event are clear: human activities and subsequent climate change. For XF, the sixth extinction will be Earth's colonization by the aliens, where the human race will be extinguished and, along with the destruction that will ensue, many species will die with it. The aliens were away, busy with more important matters across the stars; now they are returning. The entire evolutionary history of Earth has been influenced or guided by this ship towards a desired outcome (something like the current un-scientific trend: Intelligent Design). The mass extinctions were the result of the ship 'regulating' and orchestrating life, wiping the slate clean to allow for new species to develop towards the end result: Man. Perhaps even these extinctions were previous colonizations! The Purity aliens might have used Earth as a breeding ground to repopulate time and time again, returning at timely moments in Earth's history when the ship has done its job of preparing the biota for another round.

Note that the timescales involved are very great and anthropocentrism tends to summarize the 4.5 billion past history of Earth to 'something that happened before Homo sapiens'. Man as we know him only appeared about one tenth of a million years ago, roughly 3,199,900,000 years later after the first cell. It's very easy for a scriptwriter to pass on these facts very quickly. Any ship that can withstand the passage of such a long time is very powerful indeed. Let alone a species of being remaining unchanged for the same period -- we're not even sure if we'll be here in a hundred years!

The Ship: technology like magic

The ship that surfaces in an Ivory Coast coast is evidently very ancient and, for all we know, very different from anything we've encountered before. This is not a simple ship for transport or abductions. It is not 'manned'. Indeed how could it be? Its work spans billions of years, only a highly advanced mechanical emissary of alien intelligene could carry out such a long-term mission. This ship is like the monoliths in Arthur C. Clarke's novel "2001: A Space Odyssey" (1968) and its sequels (and Kubrick's filmic masterpiece). The Ship, not aliens, did all this.

The Ship manifests itself in many ways. The African fishermen, who also found the Ship fragments, were feeling its power and were afraid to approach it. Amina: "They are animists, believing nature is vengeful": animists can attribute souls to humans, animals, plants, natural phenomena, or objects (like the Ship). Their senses were more open to signals of its power, like the monkeys in Dr Barnes' lab who were upset when the fragment was revealed; people from the cities have shut their senses to anything more than the palpable. Once people start approaching the Ship and trying to learn its secrets, the Ship starts manipulating the elements to scare them away. The water around it starts boiling. Various 'miracles' reminescent of the Bible and the ten plagues of Egypt in Exodus start happening: Scully is attacked by a swarm of insects (like a swarm of locusts), the sea is painted blood red (like the Nile). The fish that Barnes lets to die in a bag come back to life: the Ship is able to play with the very basics of life and death, controlling the very basics of DNA, of healing wounds, of giving back the magic breath of life. Scully witnesses many times a very old african sage, materialized by the Ship; he is like the keeper of the Ship and tells her "Some truths are not for you" in a kind of trance-like vision Scully has. All these supernatural elements are too much not only for the African workers but for Scully as well, and the Ship is left alone.

But if the Ship is that powerful that it can heal anything, even death itself, then it's very possible Scully was healed of her ailments in the contact with this Ship here -- namely her infertility would be cured, allowing the events in 7X22: Requiem (this will be confirmed in 9X10: Provenance).

The Ship, as powerful and wilful as it may be, is however nothing more than an object. For us lowly humans, manipulated by it for millennia, we still don't have the knowledge to see beyond its tricks. Arthur C. Clarke's third law suitably states that "any sufficiently advanced technology is indistinguishable from magic". Like, again, the lunar monolith in Clarke's "2001", the Ship was activated once it reached the surface and was lit by the sun. In the end of The Sixth Extinction, the Ship has gone: it has most likely repaired itself and lifted off, which would point to the presence of nanotechnology in the alien hardware. The fragments behaving intelligently (merging, spinning, flying to the Bible) point to a decentralized technology being present and invisible in every part of the Ship: nanotechnology. Perhaps the same technology from which the nano-machines in 6X10: S.R. 819 is derived from.

The Ship: religion and powerful words

The Ship is holy, the Ship is powerful. The fact that it's the origin of life makes it holy enough, but once it created Man it also heavily influenced human culture. On the Ship, Scully finds "passages from the Christian Bible, from pagan religions, from Ancient Sumeria"; Amina Ngebe finds a "passage from the Koran: Qiyamah, the Day of Final Judgment" (the koranic equivalent to the biblic Apocalypse and the Second Coming); Dr Sandoz and Albert Hosteen had found a passage from the Genesis. Major religions seem to be originated from the Ship: the pagan and polytheistic religions of the past and the three major monotheistic religions of today (Judaism - Christendom - Islam). The founding texts of these religions are inscribed on the Ship and the manifestations the Ship is capable of served as 'miracles' to fuel belief in these religions.

Why, it might even be possible that Moses and the ten plagues of Egypt, Jesus Christ and his healing miracles, and other significant prophets and messiahs were all manifestations of the Ship! Humans are taght to be the rulers of the Earth, but only so long as they fear God, for God is the alien race that gave them life. Religions are here to pacify, to establish the basis of society but also to conform to a superior rule. We are reminded of Karl Marx's famous "religion is the opiate of the people", a drug blinding men and women from the truth and their power to be free. The passage from the Bible that Albert translated is Genesis 1:18: "And God blessed them, and God said unto them, Be fruitful, and multiply, and replenish the earth, and subdue it, and have dominion over the fish of the sea, and over the fowl of the air, and over every living thing that moveth upon the earth". The grim significance of this specific passage is that humans are taught to increase their population by using all of the Earth's resources, so that when colonization comes the Black Oil virus will make the most out of repopulating Earth.

The artifacts that Drs Merkmallen and Sandoz collect are fragments from the Ship, parts of panels that have started disintegrating and falling away from the Ship with the passage of time. Their resurfacing come as "a sign, a symbol, a revelation" that Scully ponders about in the Biogenesis teaser. In Dr Merkmallen's office, two fragments fuse together and fly to the closest Bible. The passage from the Bible that they've attempted to fuse with is the same passage that is written on them -- albeit with a different language. By pure association, the artifacts have searched and joined with the same words. The physical medium on which the words are represented makes no difference: the words themselves are the essence, the words are the power. As in readings from holy texts, in the indefatigable repetition of mantras and sutras, in the incantation of pagan phrases, the words are magic. Magic words like 'abracadabra', oftentimes translated from Aramaic as "I create as I speak", or "so be it", uttered by God when he created the World: word becomes a physical reality, word is the physical manifestation.

This is what Chuck Burks (whom we saw before in 2X21: The Calusari and 4X14: Leonard Betts and we see again in later episodes) refers to when he talks about the mystical significance of magic squares: "They first appear in the ninth century in history, but as the story goes God himself instructed Adam in their use and then handed down the secret to all his saints and prophets and wise men as a way of trapping and storing potential power to the person whose name or numerical correlative exercises that power".

Actually, the origin of the magic square is lost in legend; there are older traces in Egypt and India, but chinese traditions place its first appearance around 500 BC (Lo Shu), later feeding the mathematical representations of the Universe in Feng Shui. Passed down to the Muslims who brought it to the West around 900 AD, it was believed God had inscribed it on the seal stone of Adam's ring; it was the subject of various occult beliefs, in communication with the Cosmos, in protection from evil, as a talisman, or in the spelling of magic names using letter-numerals (abjad) -- for Jews, this was a symbol for God. This is reminding of the various attempts for the search for the name of God through the study of the Kabbalah and numerology (for this and many other matters, see Eco's "Foucault's Pendulum" (1988)). The gematria, the kabbalistic Shemhamphorasch, the tetragrammaton YHVH and others: finding the name will be a revelation, a moment of enlightenment. Knowing the name of things lends power. The words are more than a union between Man and God, but instruments for holding power over this world. Europeans lost interest in the magic square with the rationalization of the Renaissance; it was resurrected into fame recently with New Age fads and the sudoku. See also the mystery and significance of the number pi, in Carl Sagan's novel "Contact" (1985) or Darren Aronofsky's film "Pi" (1998). The magic square as a symbol, a physical projection of something larger and divine, a palpable mystery, is how the words found on the Ship should be understood.

This mixture of science and religion is something never before seen for Scully, facts that "deny all logic and reason". This Ship is "science and mysticism conjoined". Admittedly, "it's like it's the most beautiful, intricate work of art"! Spooked by the Ship's old sage and stalled by Barnes, Scully leaves Ivory Coast. Later, with the Ship gone and with Krycek cleaning up all photographic material, there is no concrete evidence of its existence. Scully (and Amina) might have seen and believed, but like with many of Mulder's investigations this makes no significant difference to the larger public.

The aliens and the Navajo

Originally, Biogenesis would not have talked about artifacts with Native American writings being found in Africa, but about the Hopi American Indians and the Australian aborigines being the only people of Earth having developed the boomerang. It all comes down to similar knowledge, writing, technology being spread in different parts the globe from one single source: the aliens. "Why would an American Indian artifact be fused in rock on the west coast of the African continent?" "It was from outer space." Similar theories of either alien visitors or lost ancient cultures that traveled the Earth (Atlantis, Ancient Greeks) have developed from observations such as pyramids being used as sacred building structures in Africa, Europe and America, or from similarities found in myths or customs of many cultures, such as the common memory of an ancient flood (Gilgamesh in Babylonians, Noah in Jews, Deucalion in Greeks, and many variations in Asia, Pacific, Americas)...

The X-Files never delved into this field, but there would have been loads of story material.

What XF tells us is that the writing of the Navajo would be of alien origin. Albert Hosteen is able to translate the writing on the artifacts, and with the help of manuals Scully as well. We are told this is "Navajo writing"; but Navajo is written with the modern roman alphabet brought by the European colonists. Chuck says that "the writing is Cree, phonetic Navajo". Cree, apart from referring to a tribe of Native Americans, is also used for the language of many Native American peoples, mainly situated in modern day Canada. These are the Algonquian languages; Navajo belongs to the Athabaskan languages. Native Americans have no writing system of their own and only held an oral tradition. James Evans, an English missionary and amateur linguist, was responsible for the creation of the Cree syllabics, or Canadian Aboriginal syllabics, around 1840 -- an artificial writing system for an already-existing language. The Cree was somewhat adopted by many peoples, even extending to some with Athabaskan languages (not the Navajo). Some peoples then claimed that the writing was a native invention pre-dating Evans -- for XF, pre-dating the Native Americans themselves. For the sake of the argument, let's say Navajo was written with Cree on these artifacts as well (it is possible, it's just that it has not been done historically), with a fancy handwriting-like font made especially for the X-Files!

Is it just the writing or the language as well? An alien source for the language would 'explain' why it is so different from anything else and why it was such a difficult code to break when the USA used Navajo to code messages in the Second World War (see 2X25: Anasazi). If the Native Americans, for one reason or another, had so much contact with the aliens that they inherited their writing, then it's possible that they inherited much more: myths, beliefs, lore. Indeed Amor Fati puts this theory forward, shedding a whole new light to the Anasazi trilogy (2X25, 3X01, 3X02) and starting threads that will be explored in depth in post-season 7 episodes (9X10: Provenance, 9X11: Providence).

The book that Diana Fowley secretly gave Scully is entitled "Native American Beliefs and Practices", a chapter of which is "The Anasazi -- An Entire Native American Indian Culture Vanishes Without a Trace -- History as Myth and end of the world symbolism. Apocalypse and The Sixth Extinction." This choice of words, shockingly fitting with the situation of Mulder and the findings of Scully, is more an amalgamation of XF elements and themes rather than true archaeology. The Anasazi 'vanishing without a trace' is a direct quote from 2X25: Anasazi. From what I gather, the Navajo and many American Indians believe that we live in the Fourth World, or the Fifth World, the ancestors emerging from successive underworlds into this one; the world above is that of spirits. The Anasazi, the Navajo and other American Indian tribes have many common points in their mythology with their older cousins from the South: the Mayas. The Mayas also believe we are in the fourth world, after the gods' three failed attempts to create a successful mankind. Experts in astronomy, they developed a Long Count calendar which spanned thousand of years. We are currently at the end of the thirteenth baktun, in a 13-baktun cycle that lasts 5125 solar years: the end of this cycle, taking place on December 21, 2012, is an important date for Mayans. This has created quite a hype in New Age beliefs, and could be compared to the XF's sixth extinction (see 9X19-20: The Truth) -- even though, for the Mayans, the end of a cycle is not necessarily bad news, but certainly a herald of change.

Scully: "It's all here, sir: a foretelling of mass extinction, a myth about a man who can save us from it..." However, the prophecy of a saviour that would save the human race from it is an invention of XF. This book Fowley gave Scully must gather apocryphal sources that are not talked about as openly to the uninitiated or that were not disclosed outside a closed circle. Albert Hosteen knew enough about Scully to trust her. Tales and prophecies that came from the aliens directly -- the whole basis of the mythology of seasons 8 & 9. And of all people, Fox Mulder is that mythical saviour of age-old prophecies. Albert: "You must find him [Mulder/saviour] before something happens, not only for his sake: for the sake of us all." How a single man can 'fight the future' through such prophecies remains to be seen (in the potential future mythological XF movies?).

Krycek's role and Barnes

Krycek is barely seen in these episodes, yet XF manage to create an entire sub-story with a couple of short brushstrokes here and there. Krycek here acts alone; since the end of the Syndicate in 6X12: One Son he has no more ties to the Cigarette-Smoking Man and can act on his own interest, even if that impinges on the CSM's policy. Krycek uses the means of pressure on Skinner he acquired in 6X10: S.R. 819, the remotely controlled nanotechnology (and the wig and beard!), to blackmail him. It's Krycek that has Skinner assign this case to Mulder & Scully; Mulder gets a sense of it when he starts hearing Skinner's thoughts ("There's someone else on this case you're not telling me"). Krycek's hopes are that Mulder & Scully, being good investigators, will uncover the evidence and find the source of these artifacts: the Ship; a logic not unlike the one he used in 4X09: Tunguska. He takes the tape of the briefing Mulder & Scully gave to Skinner and hands it to Dr Barnes.

Krycek contacted Barnes first (Barnes: "Are you the man who called?"); again, Krycek uses Barnes' passion for anything scientificoreligious to assign to him the task to follow the agents wherever their investigation might lead. Also, Scully discovers a surveillance camera in the X-Files office (placed there by Skinner under Krycek's orders?), but it won't be talked of again.

This takes Barnes to Ivory Coast, following Scully's trail. Barnes arrives at the beach revealing his true self. The whole Dr Sandoz versus Dr Barnes, the fringe theorist versus the rationalizing anti-religion fanatic and their whole struggle in the small world of Universities politics and papers seems to be poking fun at Academia! Barnes' persona as a myth-buster academic we had seen in Biogenesis is just a front he uses to gain more recongition among his peers than Sandoz, his real beliefs really are the same as Sandoz's. Barnes believes in the absolute supremacy of the Ship, he sees himself as both the keeper of the Ship as and the man who will bring this discovery to the world -- both selfish motives that the Ship will not accept. Barnes, wanting to be the only one around the Ship, kills his driver; the driver later comes back to life, looking possessed by the will of the Ship. This weak storyline ends with the driver, now the rightful keeper of the Ship, killing Barnes.

Meanwhile, Krycek is erasing all trails that can lead to the Ship. He kills Dr Sandoz; Albert Hosteen is dying anyway; he kills Michael Kritschgau, who was a major leak by sending data on the Ship to the National Institutes of Health for analysis. Skinner walks a fine line again: trying to answer to Krycek's requests, to hide his involvment to everybody else, to hide this case from Fowley who doesn't work with Krycek. He lies to Fowley about Scully's findings: "The X-File here is a fraud. Scully has ample proof of that". And in the end he tries to know as little as possible of what Scully is up to so that Krycek has less to pressure him for ("Agent Scully, I asked you not to involve me in this."). On every step of the way, Krycek is ahead of Fowley. When Fowley is reporting to the CSM on Mulder's weird condition, Krycek knows the source of the condition. When Mulder is on the floor, suffering from headaches, Krycek passes over him without assisting him: Krycek is allowing all of this.

It's possible Krycek also learnt of the prophecy and let Mulder to become a hybrid -- something that might have come in handy in the future.

But why all this trouble around these artifacts? Perhaps Krycek wants to sell them and the information around them, just as he was doing with other secrets in 3X15: Piper Maru. But it's more likely Krycek wants to recover these artifacts and to claim the Ship his own, to harness its power. Krycek's interest in the human nanotechnology he uses on Skinner might be a hint that he wants to use the nanotechnology of the self-repairing alien ships -- still, surely the alien nanotech is not what makes this Ship special, otherwise why not use any other alien ship? What is special with this Ship, in scientific terms, is not explained. The Ship is holy, and whoever has control over it goes a long way to controlling the world -- a natural for Krycek! Perhaps its power comes from the fact that the aliens themselves consider this Ship holy; a Ship that gives the miracle of life, even if it's of their own making, can only have holy connotations. Krycek's intentions would have been explored more in depth with the 'Krycek episode' that was planned for season 7 but ended up not being made...what a shame! These actions on what the CSM still sees as his own battleground will cost Krycek: next time we see him, he's imprisoned in Tunisia (7X22: Requiem).

How Mulder became a hybrid

How did it come to this? Kritschgau summarizes: "Two years ago your partner was infected with a virus he claimed was alien. A virus reactivated in him by exposure to a source of energy also alien." Mulder had been exposed to the Black Oil in 4X09: Tunguska and treated with a rough experimental russian vaccine, which killed off most of the Black Oil in him; but some of it remained, 'deactivated', rendered inert by the vaccine, basically dead but physically still present. Scully remained unaffected because though she had been infected she had been given a better, more effective vaccine (Fight the Future).

Mulder claims that his brain activity was "triggered by the rubbing" of the artifact. Scully examins the rubbing on a "charged particle directional spectrometer" (a device for determining the composition of a sample by measuring mass and charge of the sample's particles) and finds evidence of a particular kind of radiation: C.G.R., or "Cosmic Galactic Radiation", "a kind of radiation that's found only outside our solar system". What they're probably talking about is more commonly referred to as Galactic Cosmic Radiation or Rays (GCR), a radiation that originates outside the solar system from e.g. neutron stars or supernovae, high-energy particles that travel the vast empty spaces (unlike particles that originate from our Sun, that are lower-energy and do not travel as far). Most of the GCR and Solar radiation do not reach us because of the shielding of the Earth's magnetic field and atmosphere (Northern lights are solar rays entering Earth's atmosphere). GCR is indeed found in our solar system, though not originating from it. Some very high-energy energy particles are very hard to detect, and their source has been a mystery for years (research today points to black holes in the centre of galaxies as being the emitters). Finding an active source of these particles, low- or high-energy, on Earth, especially in the form of an object and not e.g. a star (!), is something Scully would have trouble explaining indeed. This radiation from the artifact, as any ionizing radiation, interferes with other matter (Dr. Merkmallen: "There was some trouble with the X-ray machine in Germany") and interfered with the rubbing with which it was in contact.

The rubbing emitted radiation that somehow interfered with the remaining Black Oil in Mulder's brain, 'reactivating' it. The Black Oil was biologically dead from the vaccine (and was already weakened because it came from Tunguska), it had no will of its own. What happened in the reactivation was different from causing the Black Oil to take over control of the body: activation is meant here in the same sense as the active genes in Gibson Praise that allowed him mind reading. The genome in the Black Oil in Mulder became active and started coding for proteins and acting like any DNA in living tissue. Suddenly, Mulder had two genomes being in action in his own body at the same time: his own and the Black Oil's. He had become a hybrid; not like Cassandra Spender whose DNA had mutated to include a mix of both DNAs, with all the green toxin and shape-shifting that ensued, but a hybrid that was supporting two DNAs simultaneously in a single organism. A human exposed to the Black Oil and then to cosmic radiation automatically becomes a hybrid. Naturally, as a carrier of the Black Oil in the first place, such a hybrid is immune to the Black Oil (CSM: "He's immune to the coming viral apocalypse!"). Evidently Mulder is the only one to have reached this status. Mulder kept his human biology (no green toxin here!) and manifested some abilities that are of alien origin: heightened brain activity, mind reading, perhaps a heightened sensitivity to anything spiritual. As Gibson was "more human than human" (5X20: The End), so is Mulder making the most out of his brain and capabilities. Scully: "He's not dying. He is more alive than he has ever been." This confirms that aliens and humans share many similar genes: Gibson read minds because some of his own genes were active, Mulder read minds because the alien genes in his brain were active. The Black Oil's genes are responsible for the mind reading, not the directly Black Oil having infected Mulder (infected people cannot read minds, see 3X16: Apocrypha, 4X01: Herrenvolk).

Brain activity and remote viewing

The effects were progressive. At first, Mulder started hearing background voices. "It comes and it goes." Mulder gets "a sense of" individual thoughts: that Barnes killed Merkmallen, that Skinner is lying. "I hear it...in my head." Then it started getting more acute, a cacophony of voices that Mulder cannot control nor direct. Then it got so intense that Mulder's brain started overloading, like a transformer that melts if too much electric power flows through it. Scully: "He's more alive than his body can withstand". Doctor: "It won't allow his brain to rest or shut down". Mulder's brain activity is painful for him and the only way he can exteriorize is violence (and calling for Scully). Doctor: "extremely abnormal brain function [...] extremely violent [...] there's activity in the temporal lobe we've just never seen." The temporal lobe is a big part of the cerebrum, dealing with sensory perceptions as vision and hearing. Mulder is given "haloperidol" to calm him down; it's an anti-psychotic drug comonly used to combat psychotic/delirium states or schizophrenia. He gives Skinner the "help me" note, a conscious move in an apparent erratic violent behaviour. From increasing brain activity and the drugs he's given, Mulder collapses into a vegetative-like state, but as we see in his desperate inner cries to his mother in the Amor Fati teaser he is still very conscious.

Interestingly enough, the Black Oil is gathered, as we learn in 4X10: Terma, around the pineal gland of the brain (the epiphysis). This area is often perceived to be the 'third eye' in various eastern and New Age religions, the 'seat of the soul' and also the organ that awaits to be activated to enable telepathic communication. This is exactly what happened with Mulder.

By this time he can fully read minds. To help him out, Mulder calls a firm and sincere sceptic and disbeliever in aliens, somebody that will only be convinced by the facts: Michael Kritschgau (from the Redux trilogy -- 4X24, 5X02, 5X03). After he exposed the conspiracy within the US government, Kritschgau's life was destroyed; he lost his son, his job and his house; he is now a conspiracy theorist on the margins of society. Kritschgau points out that the CIA ("the Company" as it's nicknamed) conducted research into ESP (Extra-Sensory Perception) to examine its veracity. This was the Stargate Project that ran after MK-Ultra,; it was based at the Stanford Research Institute and mainly ran in the 1970s, dwindling afterwards and shut down in 1995. "Remote viewing" was the term used within Stargate for clairvoyance, the ESP ability to perceive remote objects or locations. All this was explored in MillenniuM as well, in 3x02: Exegesis (predating The Sixth Extinction by one year!). Stargate was shut down because of inconclusive results, around 5-15% accuracy above statistical significance (Kritschgau: "At the CIA a high degree of ability was 20%. 25% was extraordinary."). According to Kritschgau, the "tests showed that some people have psychic abilities [...] ESP, clairvoyance, remote viewing" but not enough to justify the budget. Like with Mulder, "extreme subjects would go into arrest their minds working harder than their bodies could sustain. They became, in effect, all brain. Phenytoin was the only thing that could slow the electrical impulses to a normal rate". Phenytoin, a common antiepileptic drug, is indeed used in seizures to reduce brain activity. Here it gives Mulder enough control over his motions and his speech, but keeps his mind-reading and remote-viewing abilities intact. After all this, Kritschgau has a change of heart and is convinced of Mulder's theories: "Agent Mulder is living proof of what he tried so long to substantiate: the existence of alien life." However, the first time Kritschgau helped Mulder it cost him much; the second time it costed him his life. Kritschgau is killed by Krycek when Krycek cleans up all the evidence and collects data.

The CSM and the operation

In Biogenesis we catch a glimpse of the CSM in a big meeting around a table and we can hear a discussion taking place: "...final preparations for mass destruction on a scale that can only be imagined." "Well, what can we do to stop it?" "There appears to be nothing we can do to prevent it. It becomes a question of managing the crisis. Otherwise, we are facing annihilation ourselves." They are talking about the viral plague and the colonization! There is a map of the world in the background, with certain sites being pointed out: these could be base of operations, or the so-called alien Lighthouses (5X14: The Red and the Black), colonization hot-spots. Is the CSM trying to rebuild the Syndicate in some form with this group of (younger) people? They might be military, gathered by the CSM to be given all the secrets he's withheld for so long. What became of this later is unclear. (The supremacy of the SuperSoldiers in season 9 surely exterminated any such group.)

The CSM, takes Mulder out of the hospital to take advantage of Mulder's new condition as a hybrid, using Mrs Tena Mulder to check him out in full legitimacy. The CSM's Project doctor: "It's a chance none of us ever expected, let alone hoped for. After all these years trying to develop a compatible alien/human hybrid and to have one ready-made." Indeed it's something unexpected. With Cassandra gone and much of the hybridization research gone up in flames, hopes for finding a method of hybridization were dim. The operation the CSM organizes in a Department of Defense medical facility, using staff from he knew from the Syndicate (why else the mention in the credits as Project Doctor?), aims at making the CSM a hybrid as well. The CSM: "We're forcing the next step in evolution to save Man. [...] I'll carry the burden from here on in." The active Black Oil remainings would be extracted from Mulder's pineal gland and inserted in the CSM's; with the transfer of this active genetic material, the same hybridization process would occur on the CSM, and with the correct dosage of phenytoin the side effects of brain hyperactivity would be prevented. The CSM would succeed in becoming immune to the Black Oil!

It's at this point that we get an answer for a question that's been tantalizing fans for years: the CSM is indeed Mulder's father. The CSM might have referred to Fox as Bill Mulder's son in One Son, but this was only ideologically. Watching over Mulder in the operation room, Diana says "Like father, like son." and later "You're removing genetic material that may kill your son." Simply, like this, the answer is given. The CSM: "A father has high hopes for his son but he never dreams his boy's going to change the world." A destiny the CSM considers worthy of his son, unlike Jeffrey Spender's (6X12: One Son). (The CSM's "I'm your father" line in the teaser of Amor Fati is in Mulder's dreams.)

Despite her double allegiance to the X-Files and to the CSM, Diana still has feelings for Mulder. After Scully brought Mulder home the truth about her (One Son), Mulder must have kept his distances with her -- but he's still fascinated by his old lover, as evidenced in his dreams. Perhaps he only learned she still really loved him thanks to his mind reading capabilities here. By giving Scully the book on Navajo myths and later the access card to the DoD operation room, Diana chooses to save Mulder. The operation was complete, and it's unclear how Mulder's life was now in danger (more tests?), but he was still captive. Diana will pay this betrayal with her life. However, her death happens offscreen -- always keeping the possibility for a future return. For the first time, she betrays the CSM, and the CSM doesn't go two ways about it.

As evidenced by later episodes, the operation did not go exactly as expected (7X11: Closure, 7X22: Requiem). Anything supernatural in Mulder went away with the last drop of Black Oil that was taken out of his brain. But the CSM developed an illness that worsened his condition quickly. Perhaps it failed because of some genetic incompatibility and the CSM was not Mulder's father after all? With Mulder at hand and this being about genetics, it seems unlikely that the Project doctors wouldn't have noticed if this were the case.

The operation was a one-shot chance at getting it right, without prior experiments, and it didn't work out; the random events alone that led to Mulder becoming a hybrid were miraculous enough, wanting to replicate the result is stretching chances too thin! Or perhaps this was something that could never work in the long term: it would have destroyed Mulder but it ended up destroying the CSM instead.

When Scully talks about the prophecy, she says "that's why they [CSM] took Mulder. They think that his illness is a gift, protection against the coming plague." Scully is attributing the CSM's motives not only to Mulder's immunity against the Black Oil virus but also to the prophecy. Indeed, the CSM says: "All these years... All the questioning why... Why keep Mulder alive? When it was so simple to remove the threat that he posed?" This is a puzzling quote, to say the least. Did the CSM know all along of Mulder being the subject of this prophecy? Keeping Mulder alive despite his nosiness in Syndicate affairs was justified before by the fact that he was protected personally by the CSM: because he wanted to train him to join him at his side (5X03: Redux II). Here, the CSM seems to be saying that Mulder was kept alive so that his role in the prophecy could be fulfilled. Rewriting 6 seasons of mythology with this single quote seems too much for me. The truth may be a mixture of both: the CSM knew of the prophecy but did not know Mulder was the one until now; his motives for keeping Mulder prior to this were entirely personal -- because Fox was in fact the CSM's son. Now the CSM wants to substitute Mulder with himself in the prophecy. Perhaps the operation didn't work out because this wasn't supposed to be. There is more to the prophecy than just carrying hybrid genes -- and we don't quite know what the prophecy is. The CSM's self-indulgence is nearing blasphemy: "We're doing God's work, Diana. Without this immunity, everyone would die. This knowledge is God's blessing." The prophecy will probably not be played out in full before the date for the colonization comes, 2012.

An analysis of Mulder's dreams

Amor Fati is composed in great part of Mulder's dreams, the dreams his own unconscious mind generated when he was no more communicating with the outside world. Dreams where he "chose another path, another life, another fate". CSM: "I'm giving you a choice." This aspect of Amor Fati is most definitely Duchovny's contribution to the script; like 3X24: Talitha Cumi, a literary source is the base for the episode, here it's "The Last Temptation" (1952) of Greek author Nikos Kazantzakis, a very powerful writer (the book was also adapted in the movies by Scorcese in 1988). The controversial story has Jesus Christ -- fully human and simultaneiously fully divine according to christian religion -- letting himself be tempted by a normal life in the moment of crucifixion. He is tempted by Satan and gets off the cross, and goes on to live a peaceful married life with Mary Magdalene, to raise a family, to see Mary die; in his deathbed, he is awakened to his true mission (the salvation of mankind) by Judas, who calls him a traitor, and Jesus wanders in Jerusalem burning in the fire of the Jewish rebellion, repenting to God and rejecting Satan's offer; he then returns to the cross to die. Substitute Mulder for Jesus, the CSM for Satan, Diana for Mary and Scully for Judas, and you have the story of Amor Fati almost word for word! The Mulder-Scully exchange particularly fits: Scully: "Traitor. [...] Deserter. Coward. [...] You're not supposed to die, Mulder. Not here. [...] Not in a comfortable bed with the devil outside." Mulder: "No, you don't understand. He's taking care of me." Scully: "No, Mulder. He's lulled you to sleep. He's made you trade your true mission for creature comforts."

Mulder, for the first time, is clearly presented as the archetypal hero. CSM: "He's the hero here." Project doctor: "He may not survive the procedure." CSM: "Then he suffers a hero's fate." In his dreams, Mulder takes a break from all his worries and lets go of his quest for the truth, his winding 'fight for the future', his struggle against forces greater than him (the Syndicate and the aliens). As the CSM ponders, Mulder the hero, this complicated figure that strives for a better world, dreams of "a simpler life, full of small pleasures. Extraordinary men are always most tempted by the most ordinary things."

The dreams start in the teaser of Amor Fati. Mulder's mom visits him; and then we enter dreamland, pointed out by a sudden change in lighting and the appearance of the CSM. Everything there -- the CSM and Mulder talking telepathically, the CSM injecting Mulder, the CSM telling Mulder to "arise" and raising his hands (note how religious all this looks), the CSM telling Mulder he's his father -- are all dreams. The CSM even quotes Shakespeare ("When in disgrace with fortune and men's eyes", from his Sonnet 29). In these dreams, the CSM is his father, the one who brings him to this cozy life, the one who is always there throughout his life: he is Mulder's guide. Mulder's choice of the mysterious CSM as his father in his dreams come of course from all his suspicions that this is true (3X24: Talitha Cumi, 4X23: Demons, 5X03: Redux II) and also by the fact that the CSM is, from the beginning, perceived as the man who will lead Mulder to all the answers. The CSM takes Mulder "home. This is your new life." The perfect American Dream in a perfect suburban home. Note that Mulder has Deep Throat appear in his dreams, not X; from the beginning, Mulder has felt closer to this substitute father figure, Deep Throat, whose death had scarred him deeply (see also Mulder's near-death experience in 3X01: The Blessing Way, where Deep Throat appears as well). In dreamland, Mulder finds his sister and everyone is friendly. Diana comes to Muder's bed, in an appropriately red-lit sexual fantasy, and holds the key to Mulder's handcuffs. Fast forward through the life of a man getting married, becoming father, becoming widowed, losing everybody in his life, becoming a weakened old man.

Throughout, the CSM as the Devil dumbs the hero down to a common man no more exceptional than anybody else, inconsequential to The Powers That Be: "You can walk out of this hospital and the world will forget you." Everyone in Mulder's dream contribute to make him let go, to prove that the fight is not worth it. Deep Throat: "You can let go of all that guilt. I'm here to tell you that you're not the hub of the universe, the cause of life and death.  We -- you and I -- we're merely puppets in a Master Plan. No more, no less. You've suffered enough. Now you should enjoy your life." Diana: "You've been a child, with only the responsibility of a child to your own dreams and fantasies". In his deathbed, Mulder has aged, but the CSM hasn't changed a bit (one could almost say he's growing younger while Mulder grows older): evil is eternal, outliving everybody. "It's time for you to let go." Outside, Mulder's failure to keep commited to his quest has resulted in the apocalyptic colonization of Earth by aliens. The CSM: "There's nothing to be done. Nothing at all." In scenes where dream and reality are mixed together, Scully is given the Department of Defence access card in her apartment and she goes on to find Mulder in his deathbed -- or in the operation room. Dream Scully shakes Mulder from his lethargy and the real Scully wakes Mulder from his dream. Who is actually responsible for Mulder's salvation? Diana, Scully, or Mulder's own unconscious? Probably a mixture of all of these.

Coming between these dreams are other dreams or visions, concerning a boy on a beach -- the same beach Scully found the Ship. These are highly symbolic. The boy is not Mulder's actual son or desire of a son (or an anticipated version of William), it's a constant against which the viewer can measure Mulder's mental state. First, Mulder sees a baby taking his first steps, helped by its parents.

The baby is Mulder, taking uncertain steps in his Quest towards an uncertain goal. The CSM as the Devil/the father comes to direct him towards a specific path ("I'm showing you how to take the road not taken.") and Mulder is reminded of the baby. Later, the baby is a young boy, who says in the CSM's voice: "The child is father to the man" -- very similar to the CSM's "I'm your father". The boy is thus another father figure, a guide created by Mulder's unconscious, diametrically opposed to the CSM in age and degree of trust. Next, the boy builds a small sand replica of the Ship; the boy is Mulder's inner hope and determination for his Quest, a projection of his own resurfacing conscious desires that in the dream are rejected to the subconscious. As a wave destroys the Ship, as countless obstacles have caused problems to Mulder but never made him give up his Quest, Mulder urges the boy to start again: "You can build it again. Just start again. Okay?". After this, Mulder slowly starts accepting the simple life that the CSM/the Devil has offered him and has started giving up on his Quest. The boy has built a larger Ship, but with his own hands and feet starts destroying it; the enemy is no longer external (the wave), it's internal (oneself): "It's your spaceship. You're destroying it. You were supposed to help me." Mulder sees this scene "thousands of times", tormented by the calling of another choice in life, to continue fighting for his Quest. In the end, once back in shape, ready to continue the fight alongside Scully, Mulder has a dream that serves as a closure. The boy and Mulder both help each other to build a Ship even larger and more robust than before: Mulder's strength and determination has been renewed thanks to all these experiences. This ties back with the title "amor fati": it's latin for "love of fate", actually used by Nietzsche's "The Gay Science" (which also features a first form of "God is dead"). Amor fati refers to the fact that one should cherish all the events in one's life, happy or sad, because they have led him/her to this point in life, closer to an ultimate goal or destiny. So Mulder emerges from this humbled, but a hero still. Mulder adopts a more mature attitude to life throughout this (essentially final) season.

The spiritual world and the Mulder & Scully dynamic

So Mulder would be our saviour? This does sound fishy and misplaced in a mythology that used to be conspiratorial and science fictional at best. Perhaps the weirdest feeling comes from the change of focus: XF used to be two agents fighting for the truth against faceless and disproportionately huge forces for whom they are insignificant; a quest, though personal, directed outwards. Suddenly, the two agents become the centre of these same forces; the Syndicate the agents have been fighting against has been revealed, now the storylines are directly about Mulder (and later Scully) being major players in the grander scheme of things. And not only that, but they prove to be the subjects of prophecies whose existence pre-dates them; at such a late date, the mythology is re-written to accomodate these elements. The mystery and the logic, factual, orderly and progressive reveal of what the mythology is all about is replaced by a personal story where the untangible and prophetic (inherently unexplainable) play a big part. In the later seasons, the whole world seems to turn around Mulder & Scully -- something completely alien to the mystery of the first seasons. If there is a break in the themes and threads of the mythology, it's bewteen 6X12: One Son and 6X22: Biogenesis.

This follows a general trend from an outward ("fight the future") to an inward (spiritual) journey, in this seventh season particularly (7X07: Orison, 7X11: Closure, 7X17: all things). However, if a focus on the characters makes sense, it feels forced and out of place when the whole of the mythology, the billions-years-old plan of the aliens, the entire cosmology of the universe revolve around these two agents... Even if it's nicely executed and not very stressed here, it won't be the same in the future (seasons 8 & 9).

Here we find fan-favourite Albert Hosteen again, dying of cancer (most likely of old age -- cancer induced by handling the radioactive artifacts seems unlikely, as Drs Sandoz and Merkmallen experienced nothing such, even if it's a possibility). As in 3X01: The Blessing Way, we see the Navajo houses (hogan) and the healing 'Blessingway' ceremony being performed, this time to heal Albert. When Albert talks about Mulder ("You must find him [...] for the sake of us all"), is he discovering his nature as things are turning out or did he know Mulder was 'the one' all along? Are the beliefs and prophecies referenced in The Blessing Way and Paper Clip actually referring to Mulder specifically? This seems unlikely, not only because none of the writers had thought of such storylines yet (which is true of nearly anything in XF), but also these earlier stories of the white buffalo stand very well by themselves. Also, Mulder seems to have 'turned' into the one, through his brain activity, only recently. But what was the revelation, for Albert, that Mulder was the one? The whole spiritual communication theme is brought back from the Anasazi trilogy. Albert visits Scully in her house many times, inviting her to pray; it turns out that Albert had "been in a coma for two weeks", what Scully experienced was a visit by Albert's spirit or soul. As Albert says, "There are more worlds than the one you can hold in your hand" (this might be a paraphrase to Shakespeare's "There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy." in Hamlet, Act I, Scene V).

Interestingly enough, when Scully and Albert pray for the well-being of Mulder, Scully appears in Mulder's dreams and tries to shake him back to his quest; the figure of Scully appears as Mulder's touchstone just when Scully was trying to reach him, with all her thoughts. Albert: "You must save him." This projection of oneself through willpower resembles Mulder's visit in Scully's dreams in 3X01: The Blessing Way: souls come to contact in moments when consciousness gives way to a different plane of communication. Similarly, Albert must have discovered Mulder's role in the alien/Navajo prophecies when he entered into a coma, when his soul wandered in the search for truths unaccessible to the material world.

In these episodes, the evolution of Scully's characer is obvious: she no longer is her old rigidly sceptic self, she is now open to the spiritual world and clearly admits this can only be explained by the presence of extraterrestrials ("what's causing it may be extraterrestrial in origin" -- and Skinner answers "I know"!). She finds an entire alien ship, she witnesses paranormal phenomena (the manifestations of the Ship) and is visited by a person's spirit (Albert). As Mulder & Scully reach the end of their journey (as in 7X22: Requiem), the old believer/sceptic antithesis can no longer hold. Scully is now as defying of FBI bureaucracy and power in general as Mulder is: she leaves for Africa by herself, she rushes into Skinner's office not stopped by his secretary, she fights her way into Mulder's hospital room and saves him in the end. Scully brings Mulder back to the Quest she was not part of initially, but she has grown to be as essential to the Quest as Mulder. In his pain, Mulder asks for Scully; Scully goes to Africa for the sake of Mulder. In the end scene, Mulder & Scully announce a death of a close person to each other (Diana for Mulder, Albert for Scully) and admit that they are each other's "touchstone". The Mulder-Scully dynamic is evolving as well, heading to a much more close relationship in season 7, heading towards an end as well (particularly with the 'obstacle' of Diana Fowley gone). They both hold on to each other very much and they express it more and more -- I may be a noromo, but after so many years of partnership and the way these characters were written it's unrealistic not to adress these issues.

Wow, I wasn't planning on writing so much, but this trilogy deals with so many things!

Biogenesis


The Sixth Extinction


The Sixth Extinction II: Amor Fati