Cassandra Spender becomes the first human successfully turned into an alien/human hybrid; this heralds that the time for colonization is close, unless Cassandra is hidden from the alien Colonists. But the faceless Rebels strike again and attempt to expose Cassandra. This starts a chain of events that lead Mulder and Scully to learn the whole truth about the Syndicate: how it came to be, when, and for what purpose. The Rebels make a final offer to the Syndicate for an alliance of resistance, but the Syndicate refuses. Ultimately, the Syndicate is ambushed by the Rebels; the Syndicate and their families are burned to death. Only the Cigarette-Smoking Man, with Diana Fowley, and Krycek, secretly in league with the Rebels, escape. Jeffrey Spender proves to be an unworthy son to the Cigarette-Smoking Man, who kills him.
This is it. The whole mythology explained. Revelations so dense that these two feel like a cataclysmic series finale. With a marketing campaign selling full exposure, with scenes from "Previously on the X-Files" in the teaser of Two Fathers going back as far as 1X23: The Erlenmeyer Flask, with flashbacks to 1973 and the chronological rundown of how the Syndicate came to be and what for, this really feels like the end! After this, few questions remain. We are "fueled now with names and dates and... certainties", see files "that make all the right connections", finally hear Mulder and Scully say they "have documented evidence"! Penned by Carter & Spotnitz, with many cut scenes, and I'm sure many script drafts, this is the climax of 5 years of questions. An era is coming to an end. Of course much (if not all) was not planned when the mytharc started gaining steam in season 2. Carter & Spotnitz have been making it up as they went along, that's no secret, but what's surprising is how nicely they tie such disparate and apparently contradictory threads from 5 years together! Mark Snow's music, as with the rest of season 6, is heavily inspired/sampled from the score to Fight the Future.
The roots of the Syndicate: the 1973 agreement
The Cigarette-Smoking Man's confessions to Diana Fowley and then to Fox Mulder serve as the main exposition scenes for all the explanations -- so straightforward I'd better copy/paste the whole thing and be done with it! The conspiracy the CSM was involved with was "kept secret for over 50 years, ever since the crash at Roswell", ever since 1947.
Thus in 1973, a "majority vote" of this governmental group led to the decision to make themselves independent of the government and to collaborate with the alien Colonists. A group controlling the fate of billions, an awkward alliance with a powerful enemy. The Syndicate was born!
The aliens were probably coerced in this agreement by threats by the Syndicate that they would rather self-destroy the entire population than submit blindly. Using a scorched Earth policy and nuclear warfare in the context of the Cold War was surely within the reach of the Syndicate's capabilities. In fear of losing all their future subjects, the aliens agreed. The Syndicate would make the way for colonization, as seen in Fight the Future (the 'Project'), a great logistical nightmare that the Colonists are happy to have others handle. In exchange, the aliens would provide the science necessary for developing a hybrid immune to the Black Oil (the 'Method') to help the human scientists. The plan for the new Syndicate was no longer to try to save everyone but to save themselves, and their families. A very treacherous enterprise, but motivated by very human instincts: survival, preferential treatment, family. In face of total annihilation, survival under slavery is victory; the Syndicate is the Vichy government for the alien Reich. The agreement was passed on October 13, 1973, in El Rico Air Force Base. The choice of the 1973 date is another Carter reference to the Watergate scandal.
In addition to the science, the Method, to make hybridized genes, the Colonists provided the Syndicate with an alien fetus, fresh well-preserved samples of alien biology not in a decaying form (the Roswell bodies) or in a viral form (Black Oil): "the alien fetus would give us the alien genome, the DNA with which we could make a human hybrid." This consession was not made lightly from the Colonists' side, giving away something as personal and important to the inferior and impure humans was proof of their commitment.
Thanks to the fetus, the Syndicate could begin its hybridization effort anew, with technology much more advanced than human genetics. The project is codenamed "Purity Control". The Colonists wouldn't develop the hybrid themselves, even if it is well in reach of their capabilities; they are not the beggars in this agreement. The original fetus is safeguarded in a nitrogen tank in Fort Marlene (this is both confirmed and denied in The Erlenmeyer Flask). But the policy has changed: the conspiracy is no longer aiming to resist the aliens, no longer to make a hybrid that would fight the invaders. With a new era of collaboration, the aim for the Syndicate is to manage to survive by turning themselves, and themselves only, into hybrids. A successful hybrid would be one that would be immune to the Black Oil, but the hybrid that must be made is one using gene therapy: starting from a human being and becoming a hybrid thanks to a treatment that would not be lethal.
The exchange: the human collateral, Cassandra and Samantha
As a guarantee of the Syndicate members' loyalty, the Colonists demanded that each member hand in a person of their family. These were very "painful sacrifices", heavily symbolic, alomst like offerings to superior gods!
Bill Mulder was the "lone dissenter" of the collaboration agreement: this was a "majority vote" and Bill was of the few, if not the only one, opposing collaboration; he did not want to hand over anybody.
We see hybrids of Samantha at various ages throughout the series; hybridization and cloning permits to obtain a hybrid with the appearance of any age of the original human. It is safe to assume that all the other hybrids we see -- the young and old Kurt Crawfords, the 'Gregors', the Jeremiah Smiths -- are also clones of these original family members of the Syndicate!
The beginning of colonization
Once the successful hybrid through gene therapy would be created, the Syndicate would gather once again in El Rico Air Force Base, bringing their families, the successful hybrid and, of course, the alien fetus. They would then send a "communication" to the Colonists; the aliens would arrive to take them with them, to see that they would all be hybridized (thus rendered immune), and finally release the virus so that the colonization could begin ("They'll be transported by the colonists and begin medical preparations to receive the hybrid genes."). This process would probably happen simultaneously in other parts of the globe to take all the members of the international Syndicate. Cassandra implies that colonization would start immediately ("it all starts. There won't be any stopping it."), but we know the date is set and immutable for 2012, and that there is a predetermined "sequence of events". The Syndicate would spend the remaining time with the Colonists, waiting for Doomsday.
Buying time: the vaccine and the stalling of hybridization
The idea of resistance didn't die though. Bill Mulder ("That was your father's idea") wanted to develop a method of immunization different from hybridization: a vaccine, "to save everyone -- the World!" (the forced ironic way the CSM says this phrase shows that he doesn't believe in this at all). This concurrent project was conducted "in secret from the alien colonists". Since 5X14: The Red and the Black, Marita Covarrubias was part of this project; after many tests, she's left weak and pathetic in Fort Marlene (everybody seems to be at Fort Marlene!). This project has given some results, but not enough so that resistance can be possible.
However, "the plan was to stall, to resist": "By collaborating, you bought yourself time to secretly develop a way to combat the aliens, to fight the future." The hybridization effort is a viable plan, but only a desperate one. All hopes lie in the vaccine. The Syndicate went as far as to stall, sabotage and destroy their own work so that no hybrid is produced and the colonization can be postponed. All the efforts of Dr. Berube (1X23: The Erlenmeyer Flask) and Dr. Ishimaru (3X09: Nisei & 3X10: 731) were destroyed because they were dangerously close to success. Research was allowed insofar it didn't succeed. The experiments would be allowed to succeed in the nick of time, in 2012, to buy as much time for the vaccine research. Of course that wasn't known to the doctors working on hybrids.
Similarly, in case the vaccine research would bare no fruit, the plans for colonization had to be stalled to ensure some means of survival would exist: so long a hybridization method was not complete, the preparations for colonization would not be completed. By working slowly, the Syndicate was making sure they were necessary at all times to the Colonists -- otherwise, the Colonists would be glad to get rid of this human nuisance.
The success of Cassandra Spender
Despite of their forestalling, Cassandra Spender happened (CSM: "in spite of ourselves..."). She was taken by the Colonists in The Red and the Black to safeguard her from the Rebels setting everyone ablaze, then she was returned to the humans, and experiments on her continued as before, orchestrated by the CSM (Krycek: "Your father directs the experiments.").
Also, Cassandra develops a mind-reading ability: without any previous knowledge, she manages to understand her role in colonization; but more importantly, she manages to find Mulder's apartment (the question is asked in the script, this is not simple speculation: "How did you find us?").
When we met Cassandra in 5X13: Patient X, she was saying "the aliens were here to do good and that I was being used as an oracle to spread the word". Now she has learnt the truth and knows of colonization. This is a radical change of heart; Cassandra is no longer the smiling welcoming Patient X, she is the face of impending doom, and she will try everything to stop the Colonists. She confirms that the Samantha Mulder saw in 5X03: Redux II was not the real one: a clone. When she tells Mulder that Samantha is "out there, with them, the aliens", surely she is lying (Samantha is not there, 7X11: Closure). As time and time again, Mulder is given false hopes so that he can continue his Quest and his battle against the Syndicate.
The Rebel set Cassandra free and sent her to Mulder's, knowing that Mulder is the best way to expose the Syndicate -- using him as Krycek did in 4X09: Tunguska. When she finally realizes that her survival would mean the colonization ("when the aliens learn of Cassandra, colonization will begin"), she understands that dying is the best move for all mankind. But she didn't commit suicide -- or wasn't able to force her own hand to do it -- she asked Mulder to do it in her stead. What she didn't know is that given her nature, an alien stiletto is necessary to kill her: Mulder's gunshots would have been totally ineffective.
The Rebels strike
Amid the Syndicate's well-established plans, the Rebels happened. If their attacks in Patient X / The Red and the Black were targeted only indirectly to the Syndicate, their ultimate enemy being the Colonists, here they meddle directly with the Syndicate's affairs. There were more attacks than just the one we saw: Krycek: "Rebels have attacked and burned project facilities in New Mexico and the Southwest. The medical staff at our Arizona research facility's been slain. The train-car deaths cost us." Their target is exposure: exposing the public to all these horrible secrets, and exposing the hybrid Cassandra to the Colonists. "They saved her to expose us." "They will run medical tests on her. It's only a matter of time. Cassandra must be terminated." They want to force the Syndicate's hand to make the final choice : deliver Cassandra to the Colonists or resist.
The execution scene confirms that the Rebels need an alien stiletto to be killed, with a puncture wound at the base of the neck, 'singlehandedly' delivered by Krycek. Like in 2X17: End Game, the green toxin these aliens hold in common with the hybrids is inactive once the body is dead: the body decomposes without toxic effects on Krycek and Spender.
All bets are off
The Rebels kill one of the Syndicate members and impersonate him to infiltrate the group and make a final offer of an alliance at the point of no return: "Why not side with the rebels? Join their alien resistance?" As Krycek says, resistance is "an option you declined long ago. Resistance was futile then, why would it be any less so now?"
The CSM kept his fellow conspirators unknowing of all the facts, hoping to contain it to a close circle, but the events go out of hand and as the Rebels wanted to, Cassandra is examined (Krycek: "I recovered all the medical records form the hospital") and by the beginning of One Son all the Elders become aware of the gravity of the situation. Their stance is still the same: collaborate with the Colonists. The Syndicate thus seals its fate. It becomes but one more obstacle to the Rebels, an obstacle that must be removed. The gathering at El Rico Air Force Base sees all the important players of the US branch of the Syndicate: the Elders and their families, including the CSM and Cassandra; the dead and the departed should have been there (people like Deep Throat, Bill Mulder, the Well-Manicured Man, Dr. Openshaw, Dr. Kurtzweil, ...); also, people that joined the Syndicate later should have been all present (Fowley, Covarrubias, Krycek, ...).
The alien fetus, the possession of which secures the Syndicate's deal with the Colonists, was supposed to be taken to El Rico as well. The fetus was last seen in The Erlenmeyer Flask (or so we thought). A Rebel kills the Project doctor that was taking it and takes his appearance to join the party that takes Cassandra to El Rico. Krycek then discovers the body of the doctor (frozen by the liquid nitrogen); the fetus is nowhere to be seen, taken by another Rebel. A missing fetus can only mean that the Rebels know much more on the Syndicate than suspected, that they have infiltrated their ranks and that they're controlling the situation: Krycek: "It's all going to hell. The rebels are going to win. They took it.".
Has all the Syndicate died? It is possible similar summonings were done all over globe, where Syndicate members from all the continents convened and were ambushed -- notably we think of Strughold who is in Tunisia (according to spoilers at the time, Strughold was initially supposed to make an appearance in these episodes, but that may have been just rumours). Indeed after these episodes, the Syndicate looks dead. The US chapter of the Syndicate acted as the decisional and coordination center for the entire Syndicate, so it's more likely that the Rebels, spread thin as it is, stroke just in the USA. Cut the head and the body is left in chaos. So Strughold is likely to be still alive. Cassandra is most likely dead -- an alien/human hybrid is utterly useless to the alien Rebels.
A theory that has some credibility is that following to the events in Fight the Future, the Colonists allowed the Rebels to destroy Syndicate!
Life and Times of C.G.B. Spender
Connections are made, conspirators are revealed. "Smokey's got a name!" Scully discovers that the CSM is called C.G.B. Spender (the 'CGB' is after Chris Carter's grandpa... Charles Gengis Balthazar?), but apparently it's an alias, "one of hundreds" -- which is surprising since he's been using this name for so long (at least 1973) and officially in his marriage with Cassandra. Scully: "Cassandra Spender is, indeed, the mother of Agent Jeffery Spender and the ex-wife of C.G.B. Spender."
Strange though that Cassandra hadn't realized what was her husband's role in all her suffering: "for so many years, I didn't understand, through all the abductions and the tests, that it was you".
The CSM, as evil as he is perceived by others, sincerely believes in the righteousness of his actions ("it was the right thing to do") -- and indeed his motives make sense, in a cynical selfish way. Mulder finally gets to confront him in Diana's apartment and finally gets some answers from him.
The demise of Jeffrey Spender
Jeffrey discovers the truth as well, though he has a lot of catching up to do, and his scepticism and his disgust against anything far-fetched are of no help. When Cassandra is returned, Jeffrey is determined to find the guilty parties (the CSM is there at the train scene as well, he can be seen in the background!). Skinner advises Spender to "use every resource available", and Jeffrey doesn't turn to his father and patron in the FBI the CSM, but to Mulder -- to the great disappointment of his father. The CSM has gone to great lengths to secure a position to Jeffrey in the FBI: "I schemed to put him in charge of the X-Files".
The way the CSM sees it, the X-Files is a trial by fire for Jeffrey as it was for Mulder, a way to prove his valour and eventually join the ranks of the Syndicate as the CSM's rightful heir. The CSM puts Jeffrey to the test with various tasks ("You need to show me that you're capable of handling the responsibility that comes with this knowledge") but Jeffrey doesn't live up to his expectations. "I gave you responsibility. I gave you a position. I gave you the things that you couldn't get yourself and you can't do the job!" Jeffrey pathetically follows his father's orders but has no initiative ("I've done as you've asked", "I waited, like you asked"), and he's more than repulsed by all this patronizing and secrecy -- all this reluctance being the result of his childhood traumas when his mother was considered crazy and his father was never there (The Red and the Black). Jeffrey's past has made him a predisposed disbeliever.
When he finally discovers that the CSM is responsible for his mother's condition ("My father's involved in that?") -- by Krycek, of all people -- his turn against his father is complete. He now stands as an obstacle between Cassandra and the CSM. Aliens or not, Spender knows there is some biological hazard related to all these tests and he theorizes this is what causes the burnings: Fowley: "A contagion of unknown origin. [...] That Cassandra Spender had contracted a highly contagious vectoring organism which produces a spontaneous cellular breakdown and combustion". Jeffrey calls for the Center for Disease Control and Mulder's apartment is overrun. Jeffrey's concerns are genuine, and Fowley follows on these theories because they allow for Cassandra to be recaptured at the hands of the Syndicate.
Cassandra: "You don't understand about me." Jeffrey: "I do. I understand everything now." But he understands only part of the picture. The CSM sees this as a betrayal and after the CSM's world is shattered with the loss of the Syndicate, the CSM decides to clean house and get rid of his unworthy son. The decision is bitter: "hoping that my son might live to honor me, like Bill Mulder's son." According to Frank Spotnitz, these episodes are inspired by Coppola's "The Godfather Part II" (1974), probably in the way Don Corleone's relationship with his brother is reflected in that of the CSM and his son. A highly selfish move, but completely consistent with his character. Before being shot, Jeffrey understood who is good and who is evil and sides with Mulder and Scully. He tells AD Kersh to "do everything you can to get them back on the X-Files" and even gives a tap on Mulder's shoulder. Jeffrey was a character that was made to be unlikable from his very first appearance, constantly opposing Mulder. His final change of heart comes all too sudden and we hardly have the time to sympathize before he's gone (but for all intents and purposes, Jeffrey is dead after this!).
Diana Fowley revealed
As revealed at the end of his long soliloquies in Two Fathers, the CSM was talking to Diana Fowley. "Do you wonder why I've chosen you? You've never betrayed me. Now I need someone to trust." The CSM and Diana go back a long way, and as is evidenced by Diana touching his shoulder and the CSM visiting Diana's apartment when Mulder broke in, they were having an affair.
And then, as the CSM changes his focus from Fox Mulder to Jeffrey Spender, he calls her back to Washington to train Jeffrey to the X-Files as she had done with Mulder. She moves in the Watergate Apartments (the very same apartments from which the Watergate scandal takes its name, already seen in 2X01: Little Green Men!) -- another Carter reference to Watergate as a seat of power and plots.
Krycek and a potential resistance
We find Krycek has gone quite a few stairs up the Syndicate ladder! His progressive rise from second-hand henchman to access to the Elders' offices in 46th Street, New York is an evolution that make all his machinations and rat history pay off. But having reached such a high place by betraying everybody, his true intentions are naturally not clear cut. Before the Elders and the CSM, Krycek appears very much pro-collaboration, totally subdued, giving them praise and gaining their trust, preparing the ground for rising in power even more in the future. In a cut scene, he prods the CSM about the possibility of making him the CSM's right hand and potential heir -- but the CSM, believing in heredity, has already chosen an heir in his son Jeffrey, and puts Krycek back in his place.
As was hinted by Krycek's affinity with the Well-Manicured Man (The Red and the Black, The End), Krycek's true goal is resistance against the Colonists; despite what he may say to the Elders, an alliance with the Rebels is a good option for resistance. He is certainly not in favour of collaboration. When he kills the Rebel that Jeffrey was supposed to kill, he does so because these were the CSM's direct orders, disobedience was impossible at that time. At the end, Krycek does not appear in El Rico but stays at Fort Marlene. It's possible Krycek was in contact with the Rebels all along, aware of what was going to happen and sealing the Syndicate's fate by sending them to El Rico. But in Fort Marlene he is dismayed when he discovers that the Rebels took the alien fetus; apparently this was not part of their deal, the Rebels have betrayed Krycek in return. "It's all going to hell. The Rebels are going to win. They took it."
The roles of Mulder and Scully
In these two episodes, Mulder and Scully are purely observers and are hardly actors in the events that unfold before them at a great speed. There is no investigation to speak of, only a series of revelations and decisions made by other characters. In fact, with Patient X / The Red and the Black and Fight the Future, these episodes are the only episodes where important events in the story of the Syndicate and the mytharc actually happen before our eyes! Earlier episodes, dense as they may have been, were investigations that progressively reveal the backstory of the mytharc to Mulder and Scully, but with no significant consequence to the grand scheme of things orchestrated by the Syndicate: the investigation of a mystery. These are the revelation of the keys to unravel the mystery.
The CSM tips him with where to go if he wants to be saved: El Rico Air Force Base. Mulder uses that information not to 'save himself', but in a last desperate attempt to act and influence the events. Mulder and Scully try to block the train that carries Cassandra to El Rico; they fire some shots at the driver, apparently hit him (some say they see green blood there, but I don't think the image is that clear, and a Rebel there would make no sense when they concentrate on presenting the doctor in the train car as being the infiltrated Rebel) but the train continues unhindered. The attempt was useless, and in the end they did nothing.
In these episodes Jeffrey Spender is put in the foreground as the CSM's son, and Fox Mulder as Bill Mulder's son -- the 'two fathers' of the title. But even though we learn much of the motives behind Bill Mulder's actions, the direct subject of who Fox's real father is is not touched upon (7X04: Amor Fati will adress this directly). Indeed in insisting on resisting the CSM's offers he is indeed Bill Mulder's spiritual son, but the possibility of either as the genetic father still remains. What's more, the fact that the CSM insists so much on Fox and his superiority over Jeffrey points to the fact that the CSM really wants very badly for Fox to be his son. For the CSM, only a character as strong as Mulder's can possibly be worthy to be his son. The CSM still considers Mulder as part of the family and tips him to El Rico. In the end, only 'one son' of the two remains: Fox Mulder, the most tenacious and stubborn of the two. After all these events, Special Agent Diana Fowley is taken off the X-Files but remains in the FBI and Mulder and Scully get back their rightful place in the FBI basement. The Project, for the time being, is dead. "The future is here, and all bets are off."
The Cigarette-Smoking Man's confessions:
"This is the end. I never thought I'd hear myself say those words after all these years. You put your life into something. Build it, protect it. The end is as unimaginable as your own death. Or the death of your children. I could never have scripted the events that led us to this. None of us could. All the brilliant men. The secret that we kept so well. It happened simply, like this. We had a perfect conspiracy with an alien race. Aliens who were coming to reclaim this planet and to destroy all human life. Our job was to secretly prepare the way for their invasion. To create for them a slave race of human/alien hybrids. They were good plans... Right plans."
"I've trusted no one. Treachery is the inevitable result of all affairs."
Mulder: "The truth is out there, Agent Spender. Maybe you should find it for yourself."
Dr. Openshaw: "A man should never live long enough to see his children... or his work destroyed."
Cigarette-Smoking Man (to Jeffrey Spender): "You pale to Fox Mulder."
Jeffrey Spender: "I'll be my own great man."
Mulder's teaser voice-over: "Two men, young, idealistic, the fine product of a generation hardened by a World War. Two fathers whose paths would converge in a new battle . An invisible war between a silent enemy and a sleeping giant on a scale to dwarf all historical conflicts. A 50-years war, its killing fields lying in wait for the inevitable global holocaust. Theirs was the dawn of Armageddon. And while the world was unaware, unwitting spectators to the hurly-burly of the decades-long struggle between heaven and earth, there were those who prepared for the end; who measured the size and power of the enemy, and faced the choices. Stand and fight, or bow to the will of a fearsome enemy. Or to surrender, to yield and collaborate. To save themselves and stay their enemy's hand. Men who believed that victory was the absence of defeat and survival the ultimate ideology. No matter what the sacrifice."
Mulder: "I heard grey is the new black."
Mulder (on Diana Fowley): "Scully, you're making this personal."
Scully: "Because it is personal, Mulder. Because without the FBI, personal interest is all that I have. And if you take that away then there is no reason for me to continue."
Cigarette-Smoking Man (laughs): "Oh, you're wrong, Agent Mulder. I can't tell you how wrong you are. How wrong you've always been."
Cigarette-Smoking Man: "We would ally ourselves with the alien colonists."
Mulder: "Towards your own selfish end."
Cigarette-Smoking Man: "We forestalled an alien invasion."
Mulder: "No, no, no, you only managed to postpone it."
Cigarette-Smoking Man: "We saved billions of lives!"
Mulder: "You put those lives on hold so you alone could survive!"
Cigarette-Smoking Man: "No, Agent Mulder, so you could. That's exactly what your father failed to realize."
Mulder: "You gave them your children! You gave them your wife! You sent them away... like they were things."
Cigarette-Smoking Man: "We sent them away, Agent Mulder, because it was the right thing to do."
Mulder: "You sent them away to be tested on!"
Cigarette-Smoking Man: "We sent them so they would come back to us. Don't you see?"
Mulder: "Stop it now, or… I will stop it..."
Cigarette-Smoking Man: "No, Agent Mulder. You won't stop it. Not if you want to see your sister again."
Mulder: "You stop it... or everyone dies."
Cigarette-Smoking Man: "No. I live -- you live -- to see your sister return. It's what your father realized. It's what you'll realize as your father's son. Or die in vain with the rest of the world. (hands paper with meeting point name) Save her. Save yourself."
AD Kersh: "You have answers now? Why didn't I hear about those answers before?"
Mulder: "I've had answers for years."
AD Kersh: "Then why didn't we hear about them?"
Mulder: "Nobody ever listened."
AD Kersh: "Who burned those people?"
Mulder: "They burned themselves. With a choice made long ago by a conspiracy of men who thought they could sleep with the enemy. Only to awaken another enemy."
AD Kersh: "What the hell does that mean?"
Mulder: "It means the future is here, and all bets are off."
AD Kersh: "Agent Scully, make some sense."
Scully: "Sir, I wouldn't bet against him."
Jeffrey Spender: "I know more than enough about your past. Enough to hate you."
Cigarette-Smoking Man: "Your mother was right. I came here hoping otherwise. Hoping that my son might live to honor me. Like Bill Mulder's son." (shoots Jeffrey)