Mulder, who had been living with Gibson Praise in hiding all this time, infiltrates Mount Weather Complex and discovers the date for the alien colonization: December 22, 2012. Mulder is caught for killing Knowle Rohrer and stands accused in a staged military trial. Skinner is his laywer; Scully, Jeffrey Spender, Marita Covarrubias, Gibson, Dogget and Reyes all testify. Mulder sees the ghosts of his friends: Krycek, X, the Lone Gunmen. Mulder is helped to escape. He reaches the 'Keeper of the Truth', who turns out to be the Cigarette-Smoking Man; he is killed in a black helicopters attack. The X-Files are shut down. The Supersoldiers hold the power, preparing for colonization. Mulder and Scully are finally together but on the run.
There was a 'theory' back in the day, that Carter purposefully sabotaged his own creation so that FOX wouldn't renew XF. Even though I agree that the show did take a wrong turn and I find the theory funny to ponder at, I wouldn't go that far! There are good stand-alone episodes to be found in the last two seasons. Exhaustion and writer burnout is evident in others. The way the mythology developed and was handled in the series as a whole demanded an ending soon after 6X12: One Son; who knew that it would come three and a half years later? The Truth was a sincere but flawed effort to end the series in a nice way.
The analysis follows the breakdown of the episode. Most of the characters' testimonies really have nothing new; I will refer to the relevant episodes from which the ideas in the onscreen dialogue are explained but I will only focus on the (very) few new elements that are presented.
The testimony of Dana Katherine Scully
Subject matter: Black Oil, colonization, the Syndicate, abductions
Relevant episodes: 1X23: The Erlenmeyer Flask; 2X08: One Breath; 4X09: Tunguska / 4X10: Terma; 4X15: Memento Mori; Fight the Future; 7X03: The Sixth Extinction; 8X16: Vienen
Scully presents the biogenesis theory, that life came on Earth from pre-existing life elsewhere, from meteors that crashed on Earth. "The virus thrived underground in petroleum deposits. In black oil." This confirms that oil is nothing but a medium that the intelligent life form Purity can use to live in; since that's where it's most often found, the term Black Oil (capital letters) has been used to describe it. "It has sentience. It can think. It has the ability to communicate": to make things clear, Purity is the alien, the Colonist; Black Oil, 'creature' aliens, greys and Alien Bounty Hunters are but different incarnations that this same race, Purity, can take. "In Roswell [...] from the spacecraft wreckage [...] from their data banks they [the government] learned of the alien plan to 're-colonize' the Earth.": this Roswell data banks bit is new information, but this much could have been deducted from preceding episodes. With knowledge that colonization was coming, and that it would be spread through a virus, hybridization efforts began in 1947.
The testimony of Jeffrey Frank Spender
Subject matter: the Syndicate, the Spenders, the Mulders
Relevant episodes: 2X25: Anasazi / 3X02: Paper Clip; 3X24: Talitha Cumi; 6X12: One Son; 7X11: Closure; 9X17: William
"Samantha [...] died in 1987." In fact it was 1979. So much for continuity. "When I didn't die he [the Cigarette-Smoking Man] subjected me to the same horrible tests." Tests to make an alien/human hybrid obviously, the Project that the Syndicate has been leading since 1973. But in 9X17: William, Jeffrey says the tests done on him were to turn him into a Supersoldier. Surely the Syndicate knew nothing of Supersoldiers and the CSM would not have allowed it if he knew the Colonists had a back-up plan to replace the Syndicate members. What must have happened was that after 6X12: One Son, after much of the hybridization science and Project scientists were lost in the fire, the CSM attempted to re-create the one-time miracle of the successful alien/human hybrid, Cassandra Spender. He ordered Project doctors to work on Jeffrey. Some time after 7X04: Amor Fati he gave up. Below the decapitated Syndicate, all the infrastructure and science teams were yet intact. When the power vacuum of the missing Syndicate elders (and their official positions as government members) was filled by Supersoldiers, all the Syndicate infrastructure fell in their hands and subordinates started answering to them, conducting the humanoid Supersoldiers' projects, not knowing they were actually working against the human race. Zeus Genetics (8X20: Essence) and the Valor Victor (9X01/02: Nothing Important Happened Today) are examples of such science teams. So after his father experimented on him, Jeffrey was experimented on on the account of the Supersoldiers -- in order to find a simpler way to create a Supersoldier.
After the events of this episode, Jeffrey might have committed suicide.
The testimony of Marita Covarrubias
Subject matter: the Syndicate, the vaccine, the Rebels
Relevant episodes: 4X09: Tunguska / 4X10: Terma; 5X13: Patient X / 5X14: The Red and the Black; 6X11: Two Fathers / 6X12: One Son
"The conspirators believed all life in the universe had been infected with the virus, including a race of shape-shifting Alien Bounty Hunters who policed the conspiracy for the aliens." The theory developed after 5X14: The Red and the Black stands correct! The shape-shifters are a different race that was previously colonized by Purity; the survivors are the faceless Rebels and those infected by the Black Oil are the Alien Bounty Hunters.
After the Syndicate died and the Supersoldiers started taking power, Marita left her position in the UN and went into hiding, fearing the new power. Skinner couldn't find her. X was the one who gave Mulder the information of where she could be reached. Seeing that if she testified against the Supersoldiers lobby she would end up dead, Krycek advised Mulder not to force answers out of her. Marita was allowed to leave, probably going into hiding again.
The testimony of Gibson Andrew Praise
Subject matter: alien origins of Man
Relevant episodes: 5X20: The End
For the year Mulder has been missing, Mulder has been living with Gibson in a trailer, in Weed Hope, New Mexico, "looking for the truth", in contact with the local Native Americans. Gibson, as proof of the existence of aliens, had been hunted down by the aliens (8X02: Without) and went into hiding as well. He is able to identify Supersoldiers thanks to his mind-reading abilities, which make him a target once again.
We leave him with Doggett promising that he will protect him, but his best course of action might be to go off the grid again.
The testimony of John Jay Doggett
Subject matter: Supersoldiers, magnetite
Relevant episodes: 8X15: DeadAlive; 9X01/02: Nothing Important Happened Today; 9X08: Trust No 1
"Well, the best I can figure they're some kind of secret military project, ordinary men made invincible." We know this to be false: the Supersoldiers are an alien conscience inside a modified human body. Despite the title of the episode and the 'all cards on the table' feeling, not only the Truth is given here: each character has his own opinion of the events, an opinion based on what information he/she has available. The viewer has the privilege to be able to piece it all together. "The way I understand it the only way to kill a Supersoldier is with some rare metal. Agent Scully says it's a form of magnetite from some meteor that fell to Earth." This confirms that the metal that can kill Supersoldiers and the metal that got William rid of his growing alien powers is one and the same: magnetite. The fact that magnetite came from a meteor is an interesting info to which I come back to further down.
After Mulder's trial and Doggett's support of him, Doggett finds the X-Files office emptied of files and furniture. "They've packed up The X-Files." Obviously the X-Files face another closure, this time apprently for good. Doggett, the worthy successor of Mulder & Scully and the solid investigator of the XF cases for the past two years salvages the iconic 'I Want To Believe' poster. After this, Doggett may be reassigned to more conventional cases, but his knowledge of the Supersoldier conspiracy won't let him give up the fight.
The testimony of Monica Reyes
Subject matter: the 'organic' Supersoldier babies from chloramine, William
Relevant episodes: 8X20: Essence / 8X21: Existence; 9X01/02: Nothing Important Happened Today; 9X08: Trust No 1; 9X17: William
"Scully was one of a number of random women who had miraculous childbirths and these women all had been abducted as part of a government program": this confirms not all women are supposed to fall pregnant from the modified chloramine, only previous abductees are. "For alien babies." "To create a slave race." "Yes." This confirms that the Supersoldiers, be they the organic version babies or the adult models, are just soldiers of the alien Colonists. They may have an alien conscience dictating their moves, they are not considered by the Colonists as equals. The term "slave race" has been used before to describe the role of the classic alien/human hybrids after the colonization would take place, and indeed they would be just that: slaves that can't be killed by the alien virus, there to serve their superior alien masters. 3X24: Talitha Cumi also suggests that the Alien Bounty Hunters and/or hybrids would be used as a police force to eradicate any resistance from the human population. Presumably that's what this generation of babies that was born in 2001 is all about. Aliens infiltrated in human families with an appearance everybody would trust: 11 year old children -- even more reliable than the immune hybrids because of their alien intellect. If the Supersoldiers fill in the role of the Syndicate, then the 'organic' Supersoldier babies fulfil the role of the soon-to-be-hybridized abductees.
After these events, Reyes will be assigned off the X-Files as well but will keep in touch with Doggett. Season 9 really is the season where the relationships take the front, for good or bad. As soon as Reyes became a main character, it seems, she was changed from her independent role in season 8; she had to be given a love interest as if it were a standard thing to do with a TV character; we are far from the noromo atmosphere of the early seasons and straight into shipper territory.
The trial, Kersh and Skinner
Mulder 'kills' Knowle Rohrer, is captured and is tried for the murder of an invincible Supersoldier. The best scene of the episode is perhaps found at the beginning: the brainwashing Mulder goes through is unrelentless and exhaustive, very "1984". Kersh cooperates with the military trial because, as General Suveg reminds him, "You and I both know there are forces inside the government now that a man would be foolish to disobey": the Supersoldiers, one of whom is in the jury. The trial is a complete artifice, the outcome is pre-determined: Mulder is to be condemned to death. Skinner acts as Mulder's lawyer. After the verdict is announced, Doggett and Skinner organize an escape for Mulder -- and, unexpectedly, Kersh does "what I should have done from the start"; this is a change of heart meant to absolve Kersh of all the red tape he's been giving our agents since season 6, but it comes too suddenly. In the end, whoever supported Mulder is about to meet retribution from the Supersoldiers. The X-Files are shut down. The Toothpick Man opens the door of Kersh's office and takes Skinner in. Is this cliffhanger situation meant to imply that Kersh or Skinner or both are about to be turned into Supersoldiers as well? Have the aliens found a way to convert nicely and quickly a human into a Supersoldier without the heavy procedure we saw in season 8? If it is so, then nobody is safe! Their addition to the aliens' side would surely be beneficial and it is a frightening possibility.
The magnetite connection
Back in 2X25: Anasazi, the case of the Anasazi Native American Indians, who supposedly vanished without a trace, was explained by alien abductions. The Truth offers a different explanation. The Anasazi are an ill-defined people, ethnically; such ancient peoples lived in "pueblos" ('villages' in Spanish), or adobe birck dwellings, in what became the Southwestern States since the 12th century BCE. Mulder says they were "abandoned 2,000 years ago, nobody knows why" whereas it's more like 800 years ago, and it is officially explained by intense drought followed by migration.
The Supersoldiers, with their metal vertebra, can be categorized as biomechanical beings -- technological products. Magnetite is not only effective against them, but it seems to act against all technology tied with the alien Colonists: magnetite "like that which brought down the original UFO in Roswell". "Indian wise men realized this over 2,000 years ago." So the government knew this ever since 1947! But if magnetite is so common, why spend years researching ways to resist the alien invasion? Why the hybrids, why the vaccine? This is where Doggett's comment fits in: "the only way to kill a Supersoldier is with some rare metal [...] a form of magnetite from some meteor that fell to Earth." A form of magnetite. Not all magnetite ore is effective, only a certain kind is, with a specific range of characteristics (in crystallography terms, in iron/nickel composition in the ore, in ferrous oxides distribution, in electromagnetic properties... (although it would hardly be called magnetite if any of those were changed)) and a source of this specific kind of magnetite is meteors. Ironic that meteorites brought on Earth both the Black Oil and the means to destroy it! In Arizona, the famous Canyon Diablo meteor crater was formed from the impact of an iron-nickel meteor; perhaps the source of magnetite around the pueblo and Roswell is similar (Canyon Diablo is barely 300km away from Roswell). Also, traces of magnetite have been found and attributed to the meteor that crashed in Tunguska; the presence of magnetite would then be another reason why the Black Oil from Tunguska seemed so weakened, and thus easily to handle for vaccine research compared to other much more virulent strains.
This form of magnetite is much more rare and thus not sufficient to provide for an effective resistance against an all-out colonization effort by the aliens. Surely the US government explored that possibility, and it's likely that this is how Conrad Strughold, owner of the Strughold Mining Company (3X02: Paper Clip), was able to offer his services in the research for magnetite around the world and later become a powerful player in the Syndicate (Fight the Future).
The Cigarette-Smoking Man and the 2012 revelation
Somehow, the Cigarette-Smoking Man survived his fall in 7X22: Requiem and it would seem he got himself a nice Native American woman to do some cooking and keep him alive, probably thanks to some Indian medicine. Hippie-like, he keeps smoking his cigarettes till death do them part. This comeback is highly improbable, but a proper series ending could not have been without who was the series' main nemesis for 7 years. Pretending to be a "Keeper of the Truth", the CSM got in touch with Mulder: "I was sent a message and a key to the government facility at Mount Weather". The Mount Weather Emergency Operations Center in Bluemont, Virginia, serves as a relocation centre for the government in case of an emergency (Continuity of Operations Plan); it is a very large underground bunker that was built in 1959. It is run by the FEMA, the same FEMA that will take power over the government when a state of emergency is declared the day of the colonization (Fight the Future): "where our own Secret Government will be hiding when it all comes down". Of course, the Supersoldiers have infiltrated this nexus of power: Knowle Rohrer works there.
Mulder discovers there "the date of the final alien invasion", what is marketed as the real and only revelation of this final episode -- whereas this date could have been inferred through close examination of 2X10: Red Museum, 5X14: The Red and the Black and Fight the Future. "Ten centuries ago the Mayans were so afraid that their calendar stopped on the exact date": indeed the Mayans' Long Count calendar will end its 5125-year long cycle on this date (for the Mayans though this was not necessarily bad news, but at least an important landmark announcing changes). "December 22, the year 2012". The date is set. And the Supersoldiers, who have infiltrated all spheres of power, are keen on making sure everything will go as planned.
The CSM uses the pueblos same in the same way as those "Indian wise men" of old: "It's the final refuge. The last place to hide from those who are insidiously taking power now." Mulder and Scully's visit bring along black helicopters. The pueblo is bombed and the CSM meets his death with a CGI shot (so uncharacteristic of the X-Files) that shows his face burning so that we know he's really dead this time. The old conspirator is dead, killed by those who now enjoy his old power.
Throughout this last episode, Mulder has visions of dead people unlike any other since the beginning of the series.
These visions are reflected in Mulder's thoughts at the end: "I want to believe that the dead are not lost to us. That they speak to us as part of something greater than us, greater than any alien force. And if you and I are powerless now, I want to believe that if we listen to what's speaking, it can give us the power to save ourselves." After which Mulder touches Scully's cross. Mulder's character has evolve from somebody who believes in anything paranormal to somebody more inclined towards religion. Notice also the christian cross in Gibson and Mulder's trailer. These references to life after death and the spirits of the departed being there as sources of sanity and hope echo Commander Johansen in 3X15: Piper Maru: "We hear them [the dead] everyday. They talk to us, they haunt us, they beg us for meaning. Conscience is just the voices of the dead, trying to save us from our own damnation."
After all, the X-Files has been a story around Mulder and Scully, and the end of the series could not have not included Mulder. The result, however, is hopelessly weepy whispering scenes of reunions. Despite all these unfortunate results of storytelling dead-ends, the theme of the episode is very enjoyable: Mulder's (and Scully's) obstinacy to find this Truth, the price that comes with it and how long our weary heroes can go on making sacrifices for their endless quest. Similar themes ran through the other would-be series finales -- the Mulder-Scully motel scene in 7X22: Requiem and a short talk between Mulder and Doggett in 8X21: Existence -- and they really epitomize the hoeries' quest. If this search for a Truth is endless, if nobody will listen to the Truth when it is found, if knowledge of the Truth does not bring Justice, then what's the point? Everybody Mulder encounters tell him the same thing: this quest will end up killing him. X: "They're not afraid. They have too much power to be afraid. You're going to learn that, just like I did. You'll die learning it." Frohike: "All you're going to do is get yourself killed." The CSM: "he [Mulder] knows the truth now. [...] Now you can die."
The encounter with the CSM is like an final confrontation with the Devil. When he speaks about Mulder, he only speaks about himself: "He knows the futility of hopes and prayers". The CSM, like a vampire, justifies his whole existence and survival to that point by wanting to see the indefatigable and muleheaded Mulder giving up hope as he has: "My power comes from telling you. Seeing your powerlessness hearing it. They wanted to kill you, Fox. I protected you all these years, waiting for this moment, to see you broken, afraid." With the colonization inevitable, the last episode of the series doesn't exactly present a happy future (a state of things not different at all from 7X22: Requiem, which makes these last two seasons all the more superfluous). "The date's set. I can't change that."
But ultimately he doesn't "want to accept defeat" despite what everybody tells him and despite all that he's been through. After nine years, the roundup is grim: "what has it gotten you? Not your sister. Nothing that you've set out for. But you won't give up, even now." And Scully neither. The only thing in which Mulder has not failed with is Scully: he has opened her eyes to extreme possibilities, and she has channeled his passion. "Then we believe the same thing." The result of these nine years is that two people have found each other -- and this deep love doesn't have to express itself sexually to be fully realized (and no, it's not the noromo in me speaking, ideally this should be valid however many seasons the X-Files finally got). Such an ending was completely unpredictable at the beginning of the series; the focus and the history of the series has been written and re-written so many times that indeed at this point any noromo argument would make no sense without denying so many years of canon developments -- without forgetting though that it was these same last inferior quality seasons that tainted the reputation the X-Files had acquired. The Mulder & Scully relationship didn't kill the show -- running longer than it should have did. The magnificent motel scene (in Roswell, of all places!), beautifully lit under a falling rain, reflects Mulder and Scully's first debate in their first case together (1X79: Pilot). After 9 years of battles and suffering that left them mentally scarred and worn out, they are allowed some relief. This intimate setting is a better ending scene than the cut final scene that presented the Toothpick Man handing a paper from a kind of resistance fighters group to the President in the Oval Office. Despite the grim future the mythology of the X-Files has created for its characters, the series refuses to be pessimistic: how any kind of resistance may be realized is up for grabs, but the undefeated heroes acknowledge that "maybe there is hope".
Military Guard: "What are you thinking?"
Mulder: "Where am I?"
Military Guard: "Wrong answer! [hits wall] What are you thinking?"
Mulder: "I'm thinking about getting the hell out of here."
Military Guard: "Wrong answer! [hits Mulder] No sleeping!"
Military Guard: "What are you thinking?"
Mulder: "About my son. About his mother."
Military Guard: "Wrong answer! [hits wall] Now, what are you thinking?"
Mulder: "What do you want from me?!"
Military Guard: "Wrong... answer! [hits Mulder, Mulder resists] I want answers, you hear me? I want answers!"
Military Guard: "No sleeping! Did you hear me?" [hits Mulder]
Military Guard: "What are you thinking?"
Mulder: "What should I be thinking?"
Military Guard: "You're a guilty man. You entered a government facility illegally in search of non-existent information. You failed in every respect."
Military Guard: "Say it!" [prepares to hit Mulder]
Mulder: "I'm a guilty man. I failed in every respect. I deserve the harshest punishment for my crime."
[guard walks out without hitting Mulder]
General Suveg: "You and I both know there are forces inside the government now that a man would be foolish to disobey."
Mulder: "I smelled you coming, Clarice."
Mulder: "What are you doing here?"
X: "That's what I'm here to ask you."
Mulder: "I'm putting the truth on trial."
X: "What truth? Whose truth? You think these men will even hear it?"
Mulder: "They're afraid to hear it."
X: "They're not afraid. They have too much power to be afraid. You're going to learn that, just like I did. You'll die learning it."
Mulder: "I'm not afraid of that."
X: "There's a truth even you're afraid to speak now because you know it's futile."
Mulder: "No. Because I refuse to accept it."
Doggett: "Well, the way I look at it, calling something paranormal is just a way of avoiding a real explanation."
Reyes: "What is the point of all of this? To destroy a man who seeks the truth or to destroy the truth so no man can seek it? Either way, you lose."
Mulder: "True evil is a collaboration of men, which is what we have here today. If I am a guilty man, my crime is in daring to believe that the truth will out and that no one lie can live forever. I believe it still. Much as you try to bury it, the truth is out there. Greater than your lies, the truth wants to be known. You will know it. It'll come to you as it's come to me, faster than the speed of light. You may believe yourselves rid of your headache now and maybe you are. But you're only done it by cutting off your own heads."
Langly: "Just hang a big U-ie and never look back."
Mulder: "I can't.
Byers: "Why risk perfect happiness, Mulder? Why risk your lives?"
Mulder: "Because I need to know the truth."
Byers: "You already know the truth."
Mulder: "I need to know if I can change it."
Langly: "Change it?"
Frohike: "For crying out loud. All you're going to do is get yourself killed."
Mulder: "Yeah, you smile, feeling drunk with power. The power to do nothing."
Cigarette-Smoking Man: "My power comes from telling you. Seeing your powerlessness hearing it. They wanted to kill you, Fox. I protected you all these years, waiting for
this moment, to see you broken, afraid. Now you can die."
Scully: "Why would I accept defeat? Why would I accept it, if you won't? Mulder, you say that you've failed, but you only fail if you give up. And I know you, you can't give up. It's what I saw in you when we first met. It's what made me follow you. Why I'd do it all over again."
Mulder: "And look what it's gotten you."
Scully: "And what has it gotten you? Not your sister. Nothing that you've set out for. But you won't give up, even now. You've always said that you want to believe. But believe in what, Mulder? If this is the truth that you've been looking for then what is left to believe in?"
Mulder: "I want to believe that the dead are not lost to us. That they speak to us as part of something greater than us, greater than any alien force. And if you and I are powerless now, I want to believe that if we listen to what's speaking, it can give us the power to save ourselves."
Scully: "Then we believe the same thing."
Mulder: "Maybe there's hope."