X-Files Mythology Guide The Movie

Mythology Guide: The Movie

The Run Down:

North Texas 35000 BC; two cavemen hide in a cave during a snowstorm. Three toed footprints lead inside. One finds another caveman encased in ice and is attacked and killed by a very fast creature with sharp claws. The second caveman attacks the creature, stabbing it several times. The creature, a Mutated Grey, dies bleeding out Black Oil. The Black Oil runs along the ground then head towards the caveman. Some Black Oil on his chest forms into worms and crawls into him. The caveman begins to convulse.
Blackwood, North Texas; a boy breaks into the same underground cave and discovers an old skull. While other boys watch overhead, a Black Oil seeps out of the ground into a puddle, forms into worms and goes into his feet. He holds him arm up and sees the crawling worms underneath. The boy convulses as the Black Oil worms crawl under his skin and into his eyes. Firemen soon arrive. Four firemen are sent down into the cave and loose contact. A black helicopter arrives, carrying Dr. Bronschweig and men in Hazmat suits carrying a human sized quaratine tank. The Hazmet suited men go down into the cave and bring the boy back in the quaratine tank, and leave with him in the helicopter. The fire chief asks about his 4 men. Several large liquid tanker trucks arrive. Bronschweig calls someone; "it's Bronschweig. Sir, the impossible scenario that we never planned for? Well, we better come up with a plan".
Dallas Texas One Week Later; SAC Michaud arrives at the Federal Building which is being searched for a bomb by the FBI. Mulder and Scully are on a nearby building searched at Mulder's urging. Scully says they've closed the X-Files, they need to follow procedure and protocol now. Mulder goes to the snack room to get a soda just as a repairman leaves the room. He finds a soda machine that is lit but unplugged with no sodas; it's a very large bomb inside. The door lock has been saundered shut. Scully has the building evacuated and the door cut open with a torch. Everybody leaves the building except Michaud who stays to defuse the bomb. Mulder is suspicious. Michaud just sits in front of the bomb until it detonates, obliterating half the building in a large explosion.
Scully meets with an Office of Professional Review panel including Skinner and several Assistant Directors led by Jana Cassidy. 5 people died in the explosion; Michaud, 3 fireman, and a boy. The Attourney General is pressuring them for a report in order to lay blame as quickly as possible. Skinner tells Mulder they're looking to blame him and Scully for the explosion by not following protocol. There are talks of remediation and reassignment for them, and if they do that Scully will quit and become a doctor.
Mulder is approached at a bar by Dr. Alvin Kurtzweil "an old friend of your father's. Back at the State Department we were what you might call fellow travellers, but his disenchantment outlasted mine". He says "I've been watching your career for a good while, back when you were just a promising young agent. Before that". He is an OB-GYN doctor. He tells him Michaud didn't touch the bomb, the building was bombed because it did have some federal offices. A Federal Emergency Management Agency "provisional medical quarantine office" where the bodies were found, but the bodies were already dead. He says Michaud "was a patriot. The people he was loyal to know their way around Dallas. They blew that building to hide something, maybe even something they couldn't predict".
Blackwood; there are three large white tents set up now. Advanced machinery is in the tents and the cave entrance has been fitted with a quarantine collar. A large pipe of black liquid flows by. Cancer Man arrives by helicopter and meet Bronschweig; they don Hazmat suits and go into the cave. The fireman is barely alive, his body is becoming translucent and there is something alive in his chest and slowly moving around. Bronschweig says "we brought the temperature back down to freezing in order to control the devealopment, which is like nothing we've ever seen. [Brought on by] heat, I think. The coincident invasion of a host, the fireman, in an environment that raised his body temperature above 98.6. [The man is still alive] technically and biologically, but he'll never recover. The devealoping organism is using his life energy, digesting bone and tissue, we've just slowed the process. Do you want us to destroy this one too? Before it gestates?". Cancer Man says "we need to try our Vaccine on it". Bronschweig says "and if it's unsuccessful?". Cancer Man says "burn it, like the others".
Mulder and Scully bluff their way into the Bethesda Naval Hospital morgue where Scully examines the bodies. "There's been some kind of cellular breakdown, it's completely edematous". There's been no autopsy as reported, cause of death unknown. Mulder leaves while Scully is conducting an autopsy. The ribcage is soft and barely solid. She is forced to hide when a patrol of soliders checks the room. She tells Mulder she's found evidense of a massive unknown infection, what ever infected them had an unknown protein code and it worked extremely fast.
Mulder visits Kurtzweil's apartment; he wanted for distrubiting kiddie porn. Kurtzweil has written books about global domination conspiracies and the apocalypse. Mulder finds Kurtzweil hiding outside; he is being discredited for going to him with the truth. Kurtzweil talks about the Hanta virus, a deadly virus spread by field mice in the southwest US a few years ago. "According to the newspaper, FEMA was called out to manage an outbreak of the Hanta Virus. Are you familar with what FEMA's real power is? FEMA allows the White House to suspend constitutional government upon declaration of a national emergency. What is an agency with such broad-sweeping power doing managing a small viral outbreak in suburban Texas? I'm saying it wasn't the Hanta Virus. When we were young men in the military, your father and I were recruited for a Project. They told us it was biological warfare, a virus... We have no context for what killed those men, or any appreciation of the scale at which it will be unleashed in the future. The plague to end all plagues. A silent weapon for a quiet war. The systematic release of an indiscriminant organism for which the men who will bring it on still have no cure! They've been working on this for 50 years! While the rest of the world have been fighting gooks and commies, these men have been secretly negotiating a planned armageddon! [Negotiating with whom] I think you know. The timetable has been set. It will happen on a holiday, when people are away from their homes. The President will declar a state of emergency, at which time all government, all federal agencies, will come under the power of FEMA, the secret government". He says go to Dallas and dig.
Dallas; Mulder and Scully check the building evidense, finding bone fragments which FEMA recovered from an archeological site out of town. Scully looks at the fragments in a microscope; they have the same virus as the body. Both sets of bones are porous "as if the virus or the causative microbe were decomposing it". They learn the site of the 'dig', Blackwood.
Blackwood; the medical team is packing up, a quaratine container is readied for the fireman. It needs to be a steady -2 degrees Celsius after Bronschweig administers the Vaccine. Bronschweig goes into the cave in a Hazmat suit, and finds the fireman's chest cavity has burst open. Bronschweig tells the men up top its gestated and they run for suits. The Gestated Grey appears, screams, and attacks him, clawing at his face. He manages to stab it with the Vaccine, causing it to retreat. The men up top seal the cave entrance and bury it under dirt. The Gestated Grey again attacks him, this time holding on to him...
England; the Well-Manicured Man is relaxing in a luxureous mansion, watching a boy and two girls play outside. Cancer Man calls him; "we have a situation. The members are assembling", it's an emergency, "a meeting has been set, tonight in London to determine a course". Well-Manicured Man asks who called the meeting. Cancer Man says "Strughold. He just got on a plane in Tunis". Outside, Well-Manicured Man's grandson Matthew falls and breaks his leg, upsetting Well-Manicured Man.
London England; Well-Manicured Man arrives late at the Syndicate meeting with Konrad Strughold (a German), Cancer Man, and all the Syndicate Elders. Strughold says "we began to worry. Some of us have travelled so far and you are the last to arrive. While we have been made to wait, we watched surveillance tapes [of Mulder and Scully at Bethesda] which have raised for questions. We have been forced to reassess our role in Colonization by new effects in biology which have, presented themselves". First Elder says "the virus has mutated", Strughold says into "a new Extraterrestial Biological Entity. The geometry of mass infection presents certain conceptual reevaluations for us about our place in the Colonization". Well-Manicured Man angrily says "this isn't Colonization, this is spotaneous repopulation! All our work! If it's true, they've been using us all along! We've been laboring under a lie!". Second Elder says "it could be an isolated case". Well-Manicured Man asks "how can we know?". Strughold says "we're going to tell them what we've found, what we've learned by turning over a body infected with the gestating organism". Well-Manicured Man says "in hopes of what? Learning that it's true? That we are nothing but digestives for the creation of a new race of alien life-forms? By cooperating now, we are but beggers to our own demise". Strughold says "cooperation is the only chance of saving ourselves". Cancer Man says "they still need us to carry out their preperations". Struhold says "we'll continue to use them as they do us. If only to play for more time, to continue work on our Vaccine". Well-Manicured Man says "my lateness might just as well have been absence. A course has already been taken!". Cancer Man says "there are complications. Mulder saw one of the infected bodies that we destroyed in Dallas. He's gone there back again. Someone has tipped him. Kurtzweil we think". Well-Manicured Man says "no one believes Kurtzweil or his books. He's a toiler, a crank". First Elder says "Mulder believes". Cancer Man says "then Kurtzweil must be removed". Strughold says "as must Mulder". Well-Manicured Man says "kill Mulder, we take the risk of turning one man's quest into a crusade". Strughold says "then you must take away what he holds most valuable. That with which he can't live without".
Blackwood; Mulder and Scully arrive at the cave, which is now covered with a fresh playground and grass. At urging from the boy's friends with new bikes who were asked to be silent in return, they learn the direction that the unmarked tanker trucks went. They drive for a long time into the middle of nowhere, going on a dusty road. At night they reach a dead end and a no tresspassing sign warning murder. Scully wants to quit and return to DC for her OPR meeting. Mulder reluctantly tells her the virus is probably alien. Then a train passes in front of them, carrying the tanker trucks. They follow the train to a large valley where in the middle of a colossal cornfield are two large white domes. The train goes around the valley. They enter one dome; air rushes out the door and large cieling fans turn on at the entrance. It's cool, the temperature is regulated. Inside it is very large empty space. On either side of the middle walkway are large sealed grated boxes which make a soft buzzing sound. Mulder realizes what the sound is and they flee for the exit. Large cieling grates open, then the box grates open and thousands and thousands of bees pour out heading for the cieling. They escape but then get chased by two black helicopters with spotlights. They flee through the cornfield, and when they come out of it the copters are gone.
Scully arrives later for her OPR meeting. She presents new evidense, the fossilized bone fragments, and says Michaud was involved. As she talks, a single bee crawls around underneath her suit collar.
Mulder meets Kurtzweil; Mulder says he found a virus and an experiment involving bees and corn crops. Mulder asserts it's "a transportation system. Transgenic crops that are polygenically altered to carry a virus". Kurtzweil says that's his guess too which pisses Mulder off. Kurtzweil says he doesn't have all the answers and leaves. Mulder sees a old man is watching them from above.
Mulder goes to his apartment and finds a family picture with Kurtzweil. Scully visits; she's been transfered to Salt Lake City Utah and has given Skinner her letter of resignation. They get mushy and begin to kiss, just then Scully jerks in pain from her neck and finds a bee there. Scully reports a lacinating pain in her chest, affected motor functions, thready pulse, funny taste in the back of her throat. Mulder asserts she's going into analphylactic shock but she says she's not allergic. Mulder calls 911 and medics soon arrive. They say her throat and larynx are constricting but the passages remain open. They take her away, while Mulder keeps asking what hospital. The driver (the repairman at the Dallas building) shoots Mulder, grazing his temple. The ambulence flees as the second real ambulence arrives. Scully is put onto a cargo plane in a quaratine container with Cancer Man.
Mulder comes to and sees Skinner and the Lone Gunmen. Frohike shows the bee calling it an Africanized honey bee. Mulder switches clothes with Byers and they help him escape the hospital under a guard's eyes.
Kurtzweil waits for Mulder at the bar but runs into Well-Manicured Man instead. When Mulder later arrives, Well-Manicured Man and his driver are putting something in the car's trunk. Well-Manicured Man says Kurtzweil has "come and gone". He offers her Scully's location and cure if he gets in the car. Mulder agrees and gets the pouch; a bottle of amber serum and a note saying "Base One" and its co-ordinate location. Well-Manicured Man says "a weak Vaccine against the virus Scully has been infected with. It must be administered within 96 hours. That leaves you little time... the virus is extraterrestial. We know very little about it except that it was the original inhabitant of this planet. What is a virus but a colonizing force that cannot be defeated? Living in a cave, underground, until it mutates, and attacks. AIDS, the Ebola Virus, on an evolutionary scale they are newborns. This virus walked the planet long before the dinosaurs. Your aliens... arrived here millions of years ago. Those that didn't leave have been lying dormant underground since the last ice age in the form of an evolved pathogen, waiting to be reconstituted by the alien race when it comes to colonize the planet, using us as hosts. Against this we have no defense, nothing but a weak Vaccine. Do you see why it was kept secret? Why even the best men, men like your father, could not let the truth be known. Until Dallas we believed the virus would simply control us, that mass infection would make us a slave race. Imagine our surprize when they began to gestate. My group has been working cooperatively with the alien Colonists, facilitating programs like the one you saw. To give us access to the virus, in hope that we might be able to secretly devealop a cure. When war is futile, victory consists merely of staying alive".
(NOTE: This is a Video Release Only Scene) "Survival is the ultimate ideology. Your father wisely refused to believe this". Mulder says he let Samantha be taken. Well-Manicured Man says "no. Without a vaccination, the only true survivors of the viral holocaust would be those immune to it; human-alien clones. He 'allowed' your sister to be abducted, to be taken to a cloning program. For one reason. [So she'd survive as a genetic Hybrid] Your father chose hope over selfishness. Hope in the only future he had; his children. His hope for you, was that you would uncover the truth about the Project. That you would stop it, that you would fight the future".
He is telling Mulder this "for the sake of my own children. Once it's learned what I have told you, my life will be over... the men I work with will stop at nothing to clear the way for what they believe is their stake in the inevitable future. I was ordered to kill Dr. Kurtzweil, as I was ordered to kill you". Well-Manicured Man grabs his gun, and shoots the driver who has been listening to their conversation. He says "trust no one Mister Mulder. You have precious little time. What I've given you the alien Colonists don't yet know exists. The Vaccine you hold is the only defense against the virus. Its introduction into an alien environment may have the power to destroy the delicate plans we have so assiduously protected for the last 50 years! Find Agt Scully. Only then will you realize the scope and grandeur of the Project". Well-Manicured Man orders him out of the car, then gets back in and shuts the door. The car explodes.
Antartica 48 hours later; Mulder drives up to Base One in a snowmobile. He sees 5 small connected domes with several snowmobiles outside. He heads for it but falls through the ice into a small opening where a metal pipe sits, steam coming out of it. He goes through the pipe and ends up in a long hallway lined with cryogenic storage pods filled with snowmen encased in ice with Gestated Greys coming out of their chests.
Outside Cancer Man discovers Mulder's abandoned snowmobile. He enters the control center of the base which is filled with computers and soliders. He says "secure the station! I want everyone else down below! If you're not armed, arm yourselves! We have a breach!". Armed soliders pour down a tunnel into the structure.
Mulder comes to a colossal opening of space in the middle of the structure. At the bottom is a large hub with a middle open shaft running down, where cryogenic pods are being taken in then out via a conveyor belt. Mulder sees the cryopod with Scully's clothes and begins to descend, slipping and falling most of the way. On a platform he finds an empty quaratine container with Scully's cross and clothes inside. He checks a hallway of more cryopods; they are in water with looks of horror on their faces, a large tube stuck in their mouths. He finds Scully in a cryopod. He breaks off a piece of another cryopod and breaks open Scully's cryopod. A thick goo pours out. Mulder injects her in the shouldar with the Vaccine. Very quickly a dark thick liquid pours out of Scully's mouth into the tube, which quickly hardens then shrivels. The structure shudders.
The Base One computers mark the alarm, "there's a contaminate in the system". Cancer Man says "Mulder has the Vaccine!". The situation quickly escalates and Cancer Man orders them to evacuate. Cancer Man says Mulder will never make it out and leaves.
Mulder pulls the tube from Scully's mouth, including a thin string that was down her throat. Scully coughs out some more of the thick goo and says she's cold. Steams begins to shoot out of vents all around. Mulder pulls out Scully, puts some clothes on her, and carries her away. He comes to a vertical shaft which goes outside, he pulls her up the ladder to the first level cryopod hallways. The cryopods are defrosting, and the creatures are coming alive inside. Scully passees out and Mulder has to give CPR to revive her. They get into the pipe to outside just as the creatures break free of the cryopods. One of the creatures grabs Mulder's leg and he kicks it off. They reach the small opening. A creature comes up the pipe to attack them but a blast of steam sends it back. They make it to the surface and run as the ice begins to crack to reveal a vast crater underneath the ice. They fall into the crater, landing on the edge of the structure and sliding off it as it rises into the air. An extremely large circular UFO, the Colonist Mothership, rises and floats away. It's center underside is filled with bluegreen lights. Scully distantly tells Mulder she saw it and they hug for warmth.
Scully reports to the OPR panel. Cassidy says her official report is incomplete; though Michaud has been proved to be connected to the bombing, the other events described are too fantastic to believe. She refuses to send a report to the Attourney General and the Justice Department about bees and corn crops and Anartica. Scully says there currently isn't an investigative unit capable of investigating the things she's found. Scully gives Cassidy the bee that stung her and leaves. The panel looks at Skinner.
The cleanup: men steal the fossilized bone fragments from the FBI office. The tanker trucks get corn oil labels. Soldiers with flame throwers torch the Texas cornfield. The newspapers report a Hanta Virus outbreak in North Texas was contained.
Scully meets Mulder; she told them about her experience, how the virus is spread by bees in pollen from transgenic crops. Mulder says they've covered it all up and says she should go be a doctor. Scully says she can lives by finding out more about this virus and the cure to which Mulder had. (NOTE: This is a Cut Scene) Cancer Man watches them from afar.
Foum Tataouine, Tunisa; Cancer Man meets Strughold outside a huge cornfield holding ten or more white bee domes. Cancer Man says "we have business to dicuss". Strughold says "we have regular channels". Cancer Man says "this involves Mulder". Strughold says "ah, that name, again and again". Cancer Man says "he's seen more than he should have. He's determined now, reinvested". Strughold says "what has he seen? Of the whole he has seen but pieces. He is but one man. One man alone cannot fight the future". Cancer Man says he received telegram yesterday and shows it to Stughold; Sep 6 1998 from DC to Tunis. "X-Files reopened. Please advise".

Plot Points:

3700 years ago Texas was under an ice age and some Black Oil lived in a cave in the form of a Mutated Grey, attacking and infecting cavemen that would come by.
A boy and firemen in Texas find the same cave and becomes infected with Black Oil which has an unknown protein code. At the shock of the Syndicate, their comatose bodies begin to be consumed for the gestation of a EBE in the chest cavity. The body becomes soft.
The X-Files have been closed. Mulder and Scully are working together on domestic terrorism.
The Syndicate bombs a federal building with the infected bodies inside, which Mulder and Scully are present for and get the blame. They will be reassigned, and Scully will quit to become a doctor.
Enter Dr Alvin Kurtzweil: an old friend of Bill Mulder, he gives information to Mulder. An OB-GYN doctor who writes conspiracy and apocalypse books. He and Bill Mulder were young men in the military when they were recruited to work on a Project about a virus and biological warfare. They worked together at the State Department but he quit disenchanted before Bill Mulder did. Kurtzweil leads Mulder onto the Dallas explosion coverup but doesn't know about the bee/corn program.
Kurtzweil tells Mulder; FEMA allows the President to dissolve constitutional government on the declaration of a national emergency. A few years ago it contained an outbreak of something which it claimed was the Hanta virus. For 50 years, the conspirators have been working on the virus which will be released in massive amounts when the time comes. It will happen on a holiday, the President declars a state of emergency and the government comes under the control of FEMA.
The Syndicate keeps one infected body to test the Vaccine on. The body gestates, creating a Mutated Grey. The Mutated Grey is animalistic and very aggressive. A Syndicate doctor manages to inject it with the Vaccine, but it only causes it pain.
Enter Konrad Strughold: the leader of the Syndicate, he lives in Tunis North Africa. He was a former German industrialist.
Strughold calls a Syndicate meeting. Over Well-Manicured Man's objections, they agree to continue collaborating, to stall for time to work on the Vaccine. Stughold suggests giving 'them' an infected body and gaging their reaction. Strughold wants Kurtzweil and Mulder executed, but agree to just take away what Mulder holds most dead instead.
Mulder and Scully follow the Texas cave team to a large cornfield where bees are kept in large white domes. Mulder asserts it's a transportation system, transgenic crops polygenically altered to carry a virus.
Scully is reassigned to Utah so she quits. She almost kisses Mulder but instead a bee from the Texas cornfield stings her neck. She is taken by conspirators and flown to Anartica with Cancer Man. Mulder gets shot in the temple trying to save her.
Sympoms of a Black Oil bee sting: a lacinating pain in her chest, affected motor functions, thready pulse, funny taste in the back of the throat, constriction of throat and larynx.
Well-Manicured Man kills Kurtzweil and reveals all to Mulder and gives him the Vaccine which must be given in 96 hours and the location of "Base One" before he gets killed in a car bomb explosion.
He says: the virus is alien and the first inhabitant of the Earth. The aliens first arrived millions of years ago, some stayed behind in the form of an evolved pathogen who will be reconstituted come Colonization. They thought the virus would enslave the hosts, but they just learned the hosts would gestate a new alien. They have been working with the Colonists on their programs in order to gain access to the virus and find a cure. Without a cure the only survivors will be Hybrids and alien-human clones so Bill Mulder allowed Samantha to be taken and hoped his son would expose the Project. The Colonists do not know about the Vaccine, and its introduction into an alien environment may upset the plans of Colonization.
Mulder goes to Antartica and finds "Base One", a small computer station above the Colonist Mothership, an immense circular UFO that stores thousands of frozen humans gestating Gestated Greys. He rescues Scully and gives her the Vaccine, which causes the cryopods to defrost hatching the Gestated Greys and the UFO to lift off and fly away.
Scully reports to the OPR panel about the virus, bees, and corn but they refuse to allow the Attourney General to see it. She gives them the dead bee that stung her.
The X-Files have been reopened.
In Tunisia where Strughold lives is a colossal cornfield with ten or more white bee domes.

Analysis:

So in this Ice Cave is a living Gestated Grey and a frozen iceman. Presumably this means that a caveman wandered in the cave at some point, and the Black Oil sleeping there (left behind by the Colonists and waiting for Colonization as Well-Manicured Man tells Mulder) woke up and infected him. The caveman then gestated a Gestated Grey and died, and that Gestated Grey was running around. But in present day, the Syndicate has never seen a gestation Black Oil possession, because as they say, a Black Oil possession never occured when the hosts' body temperature was above 98.6. So in the ICE AGE how does the Caveman's body temperature rise about 98.6?!
There were three toed tracks in the snow outside the cave, so the Gestated Grey has three toes and it went running outside of the snow briefly for some reason, perhaps to find another caveman. Since a Black Oil-possessed man survives underwater without air or water or food for some 50 years, it may be assumed that the Gestated Grey doesn't require anything but its Black Oil blood.
That boy gets Black Oil worms in his arms, yet they crawled in his ankles! This means that on their way up to his eyes, some of them decided to head back down two feet into his hands then go up an extra two feet to his eyes!
We see Black Oil get through a diving suit in "Piper Maru" and Black Cancer get through a Level Four Hazmat suit in "Tunguska", so what makes these conspirators in Hazmat suits think they're safe from the Black Oil in the cave?
Bronschweig immeadiately knows the boy's infection makes 'an impossible scenario', so perhaps the boy was already turning translucent in the quarantine tank and the gestation was beginning.
Wow, isn't it amazing that Mulder manages to get the right building when there's about five buildings adjacent to the Federal Building! Mulder was not aware of the FEMA offices inside it, so it was a coincidense!
Given the amount of trouble that Mulder and Scully stirred up in "The End" which got them booted off the X-Files (of course they've done MUCH MUCH worse before without punishment!), isn't amazing that they are still partners?! In "The Erlenmeyer Flask" when the X-Files are closed they get seperated!
So Michaud was a Syndicate man, and he was deftly hoping that he could run a search on the Federal Building and survive, but when Mulder found the bomb he had to sacrifice himself to keep it exploding. Boy, he must have been really pissed at Mulder!
In its many previous appearances, the OPR Board is a completely different and smaller group of people who never get identified as Assistant Directors, yet here it's a colossal board of ADs somehow including Skinner! It this like a top-class version of the OPR which Mulder and Scully never previously warranted seeing?
Kurtzweil says he and Bill Mulder were 'fellow travellers', but as we learn in "Travellers" this refers to Americans sympathetic to the communist nations! Surely he just meant that they were disgusted with their work as Syndicate Elders.
If Bill Mulder quit the Syndicate in 1973 as he apparantly did, then Kurtzweil quit some earlier, thus he never learned about the Colonist alliance. But wait! He DOES know about the Colonist alliance, about the planned armageddon! Yet in "One Son" we learn the Syndicate didn't make this deal until 1973! An inconsistancy...?
Kurtzweil says he worked with Bill Mulder in the State Department, but then he says when they were young men in the military they were approached to work on a biological warfare Project involving the virus. So at first they were in the military, then joined the State Department? This means that when they joined the State Department, they joined the Syndicate.
So in the 1953 "Apocrypha" flashback, was Bill in the State Department yet or was he still in the military? It is an interesting connection though; Bill was first brought in to work on the Black Oil, and in 1953 we see him and Cancer Man investigating a Black Oil outbreak!
Kurtzweil is an OB-GYN doctor, which makes him an expert on female reproduction. This makes sense, since the Syndicate is mainly concerned with making a human-alien Hybrid, by the means of impregnating human females with alien sperm! Of course back then they didn't know this yet and we just preforming crude radiation and transplantation experiments, but considering that Kurtzweil was a young man in the military he probably became a doctor after he quit the Syndicate early.
Kurtzweil sure does know a lot about Michaud and the bombing consider he's been out of the Syndicate for around 40 years and is just a doctor writing kook books!
As Cancer Man walks by, a partly transparent pipe is seen, inside which a black liquid is flowing. Is this Black Oil?! If it is, it's a hell of a lot of Black Oil. Perhaps this is the Syndicate sucking up the deposit of Black Oil in the cave for experimentation. In "The Beginning" the Syndicate suddenly has a ton of Black Oil, perhaps that was just what they stole from this cave. But Well-Manicured Man later says the whole point of collaboration was to get some of the Black Oil and make a Vaccine (never mind that in "One Son" Cancer Man said the whole point was access to the alien genome, perhaps they're the same thing which would mean there is Black Oil in the alien fetus) so presumably the Syndicate already had access to Black Oil, especially since those cornfields are apparantly full it, from which Scully gets infected.
So the Syndicate bombed that building just to burn the infected bodies, presumably also to assure there would be no suspicion about their cause of death so they could quietly disapeer thanks to the military. BUT WHY BLOW A FEDERAL BUILDING?! Why not just destroy them out in the desert with no witnesses if it must be done, or just burn the bodies? If it will end up in the military anyway, why not take it directly there?! The answer of course is then Mulder and Scully wouldn't have gotten on the case!
The infected bodies are completely edematous. This means an abormal collection of liquid in the body.
Scully says the Black Oil virus which infected the firemen has an unknown protein code, yet in "The Beginning" she says she's analyzed the Black Oil virus and it is DNA and proteins are not alien. Yet they're unknown but not alien!
So a few years ago there was another Black Oil outbreak in Texas handled by FEMA? Presumably it's just another cave full of a Black Oil deposit found, yet why didn't this one end up with a Gestated Grey? Perhaps it happened during winter so it wasn't hot enough.
So the Syndicate began around 1945 with Roswell, so presumably this was around when Bill and Kurtzweil were approached to work on the Black Oil. So there Black Oil in the Roswell wreakage!
If this Black Oil created a gestation just by the coincidense of high temperatures (of course this is the Syndicate theory it could be wrong perhaps it is a conscious decision on the part of the Black Oil) how does it expect it all to create gestations come Colonization? Perhaps the Colonists are accelerating global warming so that 2015 it is very hot everywhere. For example what about people living in the artic regions? Even in high summer it's freezing there!
Why does Bronschweig want to keep the fireman in subzero temperatures after the Vaccine is given? Don't they want to know what will happen under normal temperature conditions when the Vaccine is administered to an infected human?
The Gestated Grey is just about human sized at maybe five feet. So how in the hell did it come out of the chest cavity of a six foot man?!
Bronschweig injects the Gestated Grey with the Vaccine, which causes it pain and makes it retreat for a time. That's why it's a weak Vaccine, it only works on people infected with the Black Oil. But it did cause it considerable pain, just not enough to kill it. It must be like it's blood is on fire. And when Mulder introduces the Vaccine into the Colonist Mothership, it causes pain in all the other Gestated Greys and the ship itself.
Why is the Syndicate burying Bronschweig and the Gestated Grey alive? Isn't there a serious problem of exposure? Boy, it's a good thing Mulder didn't rally up a construction crew to dig under the playground, or he'd have a Gestated Grey on his hands and physical proof of alien existance!
Strughold at first keeps talking about rethinking their role in Colonization, but then he just decides to keep collaborating!
Strughold offers to give the Colonists one of the infected bodies, presumably to gage their reaction. First of all, this proves once again the existance of the Colonist Radio and how the Syndicate uses it. Second, it means that whoever the Colonists send as an ambassador or sorts will have human expressions or how else can you gage their reaction? Perhaps they would send a Pilot, who of course wears a human face and so has human emotions.
Well Strughold knows about the Vaccine, and by talking about it in front of those ten odd Elders it means they all do as well. Yet in "Terma" Well-Manicured Man said to Cancer Man that only six of "us" knew about the Vaccine Program! Then again maybe this has changed since Krychek gave Well-Manicured Man the Russian Vaccine in "The Red and the Black".
Well-Manicured Man definitly seems inferior in power to Strughold, and in fact he seems inconsequential in his vote compared to the rest of the Elders. Yet he seems to be the leader of the Syndicate in every episode prior to this! Perhaps he was the ipso facto leader since Strughold seems to prefer to chill in North Africa, leaving administrative duties to the rest, but has now fallen out of favor after his controversial push for resistance in "The Red and the Black".
That fact that Mulder saw an infected body alters their decision about rethinking their role in Colonization?! How?! As Strughold says at the end, he is but one man and one man alone cannot fight the future!
So Strughold orders the execution of Scully; later she is bitten by a Black Oil bee which hides in her collar for hours and hours, then waits until she's about to kiss Mulder before stinging. Obviously the bee is under the remote control of the Syndicate, and whoever is controlling it is following Strughold's orders. This harkens back to the Hybrids can telepathically control the bees theory which is strongly suggested in "Herrenvolk".
So what was in those unmarked tanker trucks? Presumably lots and lots and lots of Black Oil, that must have been a HUGE deposit in that Texas cave! Where where the tankers taken? The trains carrying them are last seen going around the valley where the cornfield is, so presumably they just get taken to a Syndicate Project facility somewhere. In "The Beginning" and "Two Fathers" we hear reference to a Project Arizona Research Facility where the Black Oil is being worked, presumably it was taken there.
So Black Oil is somehow placed into the cornfield, like the flowering shrub seen at the Project farm in "Herrenvolk". These bees, genetically altered to carry the Black Oil without being affected themselves, are then released and sent to harvest pollen from the corn, thus carrying the Black Oil. These bees can then be released and controlled by the Hybrids to infect the majority of humanity.
How do they get the bees back in their enclosures? Hybrid telepathic control!
So why do those helicopters stop chasing Mulder and Scully once they get out of the cornfield? They let them escape so Mulder would survive and Scully would escape with a Hybrid-controlled bee in her collar.
Mulder says the crops are polygenetically altered. Poltgenetically roughly means of more than one kind, in other words Hybrid!
So Kurtzweil knows Black Oil will be distributed to humanity come Colonization, which the Syndicate is collaborating with the aliens on. But he doesn't know about the bees and corn?! This must be a recent (post '73) devealopment, but he shouldn't even know about the collaboration bit!
Then again, perhaps Kurtzweil became a doctor then got drafted into the military for WWII and then joined the Syndicate in 1945, and continued work with them until 1973 when at the first mention of collaboration with the Colonists he quit. Bill Mulder felt the same way, but he stayed on just a tad longer.
So the same man who planted the bomb is also now driving the ambulence which steals Scully? Boy, that Syndicate must be really starved for assassin / clean-up talent!
Why does Cancer Man decide to go down to Base One with Scully?
So the bees come from Africa; so does Strughold! Perhaps the bees are genetically manufactured there then shipped out.
Well-Manicured Man killed Kurtzweil. Even if Kurtzweil was alive in that trunk when he was put in, that same car exploded in a big car bomb explosion a little later, so he is definetly dead.
Let's say Mulder was out for about 4 hours after being shot in the temple. That means that after being infected with a bee-amount of Black Oil, you have around 100 hours to administer the Vaccine before it becomes irreversable.
So the Black Oil virus was the first inhabitant of the Earth. Life began around 4 billion years ago with single celled organisms in the sea. Are these the one and the same?
The Black Oil virus is the first inhabitant of Earth, which makes it around 4 billion years old. But the aliens first arrived only million of years ago. This means they are not the same thing, yet some of the aliens stayed behind IN the Black Oil virus. The best explanation is that Earth was first given life 4 billion years ago by the Colonists, who seeded it with the beginnings of Black Oil. Life devealoped from this, humanity is a descendant from the Black Oil virus. Since we know from "Two Fathers" that the Colonists ARE the Black Oil, this must be true, the Black Oil can't just be something the Colonists found and took over on Earth.
Even back then before the dinosaurs, the Black Oil virus was possessing creatures and using them to walk around. Of course this means that back then they weren't using animals to gestate just to possess like in "Piper Maru", or perhaps humans are the ultimate descendant created by the Colonists to be a perfect vessal for Black Oil and thus things like dinosaurs and reptiles their ilk are incompatible for gestation.
If this is true, then uncommon alien species would also be incompatible for gestation, yet Cassandra says in "Two Fathers" that the Colonists are invading all over the universe. So this must mean that the Colonists are the first or among the first intelligent lifeforms in the galaxy, and they seeded many other worlds in order to create the perfect vessals for their Black Oil.
Well-Manicured Man says that only human-alien clones will survive the viral holocaust, yet in "One Son" we learn that the Syndicate Elders and their families will be given the Hybrid genes so they can survive! Furthermore, won't Hybrids survive as well? Or are all Hybrids clones of each other using female abductees?
So Well-Manicured Man hopes the introduction of the Vaccine "into an alien environment" may upset Colonization. Mulder does this and it makes the Colonist Mothership retreat. Obviously Well-Manicured Man knew how the Colonist Mothership was like one big living organism with all the Gestated Greys in stasis like body cells.
So why does the car explode? Perhaps before dying the driver activated a car bomb so that when the rear doors were opened then shut they would detonate. Obviously Well-Manicured Man knew this would happen, why else would he get in the back seat? If he intended to drive the car away he would have gotten in the driver's seat.
So Mulder flew to Antartica, rented a snow mobile near Base One and drove all the way out there, with Cancer Man unaware. Surely there's only one snowmobile rental place in the area, and surely Cancer Man would have it under surveillance!
So a pipe was running out the Colonist Mothership releasing steam, which melted a chamber of ice creating a snowtrap, which Mulder falls through. Presumably there are a lot of these around. When the Colonist Mothership took off and presumably went into space, these pipes must have been closed or else the air inside would rush out!
So Mulder entered the Mothership at the top levels, which are the oldest. It holds infected humans from 3700 years ago, so that's how long the Mothership has been buried in the ice gathering infected humans. At the bottom are the more recent, including Scully. In fact, the Mothership seemed pretty close to filling up. This makes sense, since Colonization is only about 15 years away and it has 3700 years worth of infected humans!
Mulder sees a Gestated Grey in one of the cryotubes. So the Syndicate keeps observation on the Mothership, and if they were allowed inside they must have surely seen the Gestated Grey and thus known about gestation but they didn't! This must mean the Syndicate personnel are not allowed in the Mothership, or at least the older levels. Maybe there is a chute where they are instructed to toss in cryopods with infected humans, and they never step foot inside the Mothership but have computers that watch it.
So why is the Mothership collecting infected humans? They seem to be infected by happenstance, accidently coming across a Black Oil deposit. Then again, there must millions of people in there. Then again then again, it has been there 3700 years. Perhaps it takes any people infected to make sure the humans don't learn about the gestation thing, but that means they are assuming that come 2015 there will be a centralized human secret government which will offer to collaborate, more likely its just a general practice so the mice don't know they're about to fed to the snake. If this is true, there must be A LOT of Black Oil deposits lying underground!
Will this big collection of Gestated Greys play a role in Colonization? Or perhaps they are just part of the new alien population.
Or perhaps at the top levels are the ancient people accidently infected, then most of it is taken up by people gathered purposely by the Syndicate, but we've never heard of this before people being permenantly taken.
Cancer Man sends armed men down into somewhere when Mulder shows up. Does this mean into the Mothership, or just the lower levels of Base One? Perhaps he is sending armed men to apprehend Mulder and pull him outta there, but then that means the Syndicate personnel are allowed inside the Mothership and thus they would know about gestations.
There is a long shaft running down at the center of the main area of the Mothership. When we see the underside of the Mothership, there's no big hole at the middle so Mulder only saw perhaps the top half of the Mothership!
So an automated system carts cryopods into the middle hub then takes them back out again. What it done to them inside the hub? Perhaps they are just checked on by automated systems to make sure they're not gestating or anything.
At a lower platform near a conveyor belt, Scully's empty quarantine chamber is sitting with her clothes inside. This suggests that there was some Syndicate personnel in here who stripped her naked and threw her in an alien cryopod, so perhaps they're allowed in but not on the upper levels just the 'loading platform'.
But then again Base One sits on top of the Mothership, and the ancient cryopods are on the top levels, so how could they avoid them while getting to the 'loading platform'? Perhaps an elevator takes them down to the middle of the Mothership.
That liquid that fled Scully must have been the Black Oil and possibily just beginning to devealop organism. Notice that it seemed to shrivel and die as it left. In "Patient X" we see that Black Cancer given the Vaccine survives and can infect another host, so perhaps because it had already begun to gestate it was killed, ie it had already begun to infest itself into her body so it died when it was suddenly forced out.
This explains why the Mothership reacts so horribly to the Vaccine into its system. All of the Black Oil in the Mothership had already begun to infest itself into the hosts, so it was in a vunerable state. When Mulder injects the Vaccine, it quickly spreads to every single cryopod because the Mothership is like one big body with every cryopod a body cell. It would have killed every 'body cell' if they didn't disconnect themselves before the Vaccine filtered into their system.
Why was a tube running all the way down Scully's throat, probably into her stomach? It probably had something to do with the fact that that's where the Gestated Grey is created.
Why did steam shoot like that? The Mothership automated systems (an artificial intelligence of some kind?) sensed the Vaccine, so they turned up the heater so to speak to defrost the other cryopods so the Gestated Greys could hatch and escape before the Vaccine filtered to them and killed them.
So Mulder dragged Scully vertically up the entire heighth of the main chamber?! He entered at the top and ended up at the bottom of the main open chamber, and that looks like about thirty stories tall! Hopefully he found an elevator!
If you listen carefully Scully whispers to Mulder that she saw the Mothership as it floated away. Now how in the hell can she not believe in aliens after seeing such a freakin' big UFO?! Well she could always write it off as a dazed hallucination...
When Cancer Man visits Strughold, Strughold seems annoyed that he's here and says they have regular channels. This supports the fact that Strughold doesn't want to be involved in the administrative duties of the Syndicate, he tries to be away from it as much as possible. It's also an almost semi-credible explanation why Strughold never appears on the television episodes!
So thanks to Scully's showing of evidense and Skinner's urging, the X-Files were reopened. But as we hilariously learn in "The Beginning", Mulder and Scully don't get assigned to the X-Files and are still working domestic terrorism!

In the Movie DVD Commentary, Cris Carter and Rob Bowman reveal hidden plot points about the Movie: the Mothership UFO at the end has been there since the Neanderthal Period; in fact the first cryotubes Mulder encounters hold Neanderthals, but the camera couldn't pick this up. The Vaccine hurts but does not kill the aliens; Bronschweig injects the Gestated Grey with it, and it momentarially pauses in its attack. When Mulder injects Scully with the Vaccine, the Black Oil is expunged. The reason steam erupts and the aliens gestate is because the system is trying to 'hatch' the aliens before the diluted Vaccine gets into them and kills them.

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