The colonization of Earth was the end game in the Syndicate's Project, in collaboration with a race of alien colonists. (TXF: "The Truth", et al.) According to conventional human science in 1993, the introduction of an alien life form to the planet Earth was the only element that could prevent humans from living out their days as rulers of the world, as the latter possibility was virtually insured by human intelligence. (TXF: "The Jersey Devil")
After arriving prehistorically, aliens who had not left Earth prior to the planet's last ice age awaited colonization, lying dormant underground in the form of an evolved pathogen, waiting to be reconstituted by the alien race of colonists when they came to colonize the planet, using humans as hosts. (The X-Files Movie)
The US government first learned of the aliens' plan to re-colonize the Earth in 1947, when the humans salvaged various alien technology and captured aliens from spacecraft wreckage in Roswell, learning of this plan from the craft's data banks. Fearing that wild panic would erupt if knowledge of the colonization plan was publicly released, the government purposefully kept this information secret. One of the men who learned of the colonization plot was President Truman, the first of many presidents who learned of the event and was scared of it. (TXF: "The Truth")
- In a section of dialogue cut from "The Truth", it is revealed that the government men who knew of the colonization plan threatened the aliens that they themselves would use the newly developed atomic bomb to destroy the Earth and render it uninhabitable for alien life. It is also said that this threat of annihilation bought the men time.
The Syndicate secretly came together at the State Department on the project that dated back to Roswell. (TXF: "One Son") They originally believed, however, that the alien virus would simply control humanity and that mass infection would make humans a slave race. According to former Syndicate member Alvin Kurtzweil in 1998, the Syndicate had started secretly negotiating "a planned Armageddon" about fifty years earlier, while the rest of the world had fought "gooks and commies". (The X-Files Movie)
In the 1950s, men like Syndicate member William Mulder collected information, including genetic data, in adherence with government instruction to gather the data for the purpose of post-apocalyptic identification due to the threat of nuclear holocaust at that time. These records still remained in 1995, however, hidden at the Strughold Mining Company, and contained decades' worth of information pertaining to abductees, such as Samantha Mulder and Dana Scully, the files being an indication that the Syndicate was preparing for the future alien colonization. (TXF: "Paper Clip")
In 1973, the Syndicate took a vote that changed the fact that, rather than continuing to cleave to a government agency, they would now operate privately, on their own Project, and they agreed, by a majority vote, that they would cooperate with the alien colonists. (TXF: "One Son") William Mulder disagreed with this decision, however, and opposed collaboration as a means of surviving the forthcoming colonization. (TXF: "Two Fathers", "One Son") He refused to believe that survival was the ultimate ideology. (The X-Files Movie) As the lone dissenter in the group, William Mulder said that allowing colonization to begin would be the Syndicate's "tragic mistake". He railed at the group's other members and their plans, even as the rest of the group sent members of their families away to the aliens, in exchange for the only thing necessary for the Syndicate to proceed - an alien fetus that would give them the alien DNA with which they could make a new race of alien/human hybrids, so that certain humans would survive the holocaust. At about the same time, however, William Mulder came up with the idea of stalling and resisting the alien colonists, to work secretly on a vaccine, using the alien DNA, in the hopes that such a vaccine would save humanity. This idea influenced William Mulder to finally come along with the Syndicate. (TXF: "One Son")
He eventually came to realize and accept that such a familial sacrifice, the like of which the other group members had already made, was necessary for humanity's survival. (TXF: "One Son") Because the only true survivors of the viral holocaust, without a vaccination, would be human/alien clones immune to the virus, William Mulder allowed his daughter, Samantha, to be taken to a cloning program so that she would survive as a genetic hybrid. (The X-Files Movie) Due to the fact that William Mulder was late to understand the need to give up one of his children to the alien colonists, however, Samantha was abducted from the Mulder family home, right in front of her brother, Fox. (TXF: "One Son") William Mulder also hoped that his son, Fox, would ultimately fight the future. (The X-Files Movie) Indeed, Fox Mulder was an integral part of the equation (including its end result), as the Cigarette Smoking Man would later remind an alien bounty hunter, in 1996. (TXF: "Herrenvolk")
Lead-Up to ColonizationEdit
In 1995, the Well-Manicured Man obliquely referred to the Syndicate's insidious plans for the future when he - during his first meeting with Fox Mulder's FBI partner, Special Agent Dana Scully - told her that his group predicted the future and that the best way to predict the future was to invent it. (TXF: "The Blessing Way")
Shortly thereafter, Scully and Mulder discovered the hidden files at the Strughold Mining Company and the Well-Manicured Man told the agents about the origin of the files, Mulder essentially realizing - by noting that the documents included current information about abductions and abductees - that the group who had gathered them were preparing for a forthcoming Armageddon. (TXF: "Paper Clip")
Later that year, the Well-Manicured Man expressed to the Cigarette Smoking Man that he feared that security of their Project's future would be compromised beyond repair if Syndicate operative Luis Cardinal was identified by FBI Assistant Director Walter Skinner, who Cardinal had recently shot, as the Syndicate's well-placed operatives would consequently not be able to prevent Cardinal from being arrested, thereby also permanently compromising the secrecy of the Syndicate's work. (TXF: "Apocrypha")
While questioning an imprisoned Jeremiah Smith in 1996, the Cigarette Smoking Man commented that the prisoner and those of his like were not allowed to put their indulgences ahead of the "greater purpose", but the prisoner claimed he no longer believed in that. Near the end of this conversation, the Cigarette Smoking Man replied, to Smith asking what the cost to humans would be if the Project was to go forward, that the question was irrelevant and that the outcome was inevitable, adding that the date was set. Jeremiah Smith also implied that, in the same aforementioned outcome, many would die at the hands of the Cigarette Smoking Man to preserve his stake in the Project, just as Deep Throat had already done.
Jeremiah Smith, physically disguised as William Mulder, later passed judgment on the Cigarette Smoking Man by remarking that all he wanted was to be part of it, to be one of the commandants, when the process would begin.
Shortly thereafter, X told Agent Mulder that the value of a gimlet weapon would soar, the need for such a weapon becoming desperate, when the time came and the truth was finally determined. Even though Mulder asked X to confirm that he was referring to colonization and wondered if his own conclusion that the date was set was accurate, X did not directly answer Mulder nor verify his suspicions. (TXF: "Talitha Cumi")
Shortly after Jeremiah Smith escaped, he privately told Mulder, "I must perish. Whatever the consequences to that end, they are incalculable to the preservation of the larger plan." Mulder initially thought that the larger plan of which Smith spoke was a reference to colonization, but Smith explained that he was actually referring to hegemony and a new origin of species. Because Mulder still did not understand, Smith took him to Canada, to demonstrate an agrarian work force of child clones who were a mixture of blond boys and girls who looked identical to Mulder's sister, Samantha. (TXF: "Herrenvolk")
Moments after Agents Mulder and Scully discovered that Alex Krycek had apparently been assisting a group of political bombers, Krycek told the agents that the members of the Syndicate were "the engineers of the future" and "the real revolutionaries." (TXF: "Tunguska")
In 1998, faceless aliens, who opposed the alien occupation of Earth, were responsible for several mass burnings of abductees at sites that would ultimately serve as alien lighthouses where colonization would begin, such as Kazakhstan, Skyland Mountain and Pennsylvania's Ruskin Dam. By this time, the Syndicate had learned that, in the final stages before it would begin, there would most likely be assemblies and group abductions, and that the alien 'black oil' virus would be unleashed on a major scale during colonization. The Syndicate members argued amongst themselves, not only about the meaning of the recent attacks but also, after they acquired a vaccine for the black oil virus and captured one of the faceless aliens, about the best method of resistance regarding colonization. (TXF: "Patient X", "The Red and the Black")
Soon thereafter, Krycek finally confirmed for Mulder that the planned alien invasion was arranged but Mulder, whose entire belief system had recently changed, was at first merely amused by Krycek's claims. Krycek also revealed to Mulder the actual motive behind the recent mass incinerations and, even though Krycek believed that the resistance against the aliens would die if the captured faceless alien died, Mulder failed to stop an alien bounty hunter from intercepting the alien captive, both extraterrestrials apparently disappearing simultaneously, while an observing Mulder was temporarily blinded by an intense white light. (TXF: "The Red and the Black")
Later that year, Mulder concluded a drunken screed in which he miserably described himself to a barmaid at Casey’s Bar & Grill by mentioning that he was known to chase after aliens, shouting to anyone who would listen "that the fix is in, that the sky is falling and when it hits, it's gonna be the shitstorm of all time."By this time, former Syndicate member Alvin Kurtzweil had written at least two apocalyptic books - The Four Horsemen of the Global Domination Conspiracy and Countdown to the Apocalypse - but recognized his books by Mulder's description of them, in 1998, as "end-of-the-world apocalyptic garbage". Moments after Mulder used this description, Kurtzweil told him that, in the future, the alien virus would be systematically unleashed at a scale neither man had any appreciation of and that the men who would bring it on had been secretly negotiating a planned Armageddon.
Kurtzweil explained that the timetable had been set and detailed the process by stating that it would happen on a holiday, when people would be away from their homes. According to Kurtzweil, the President would declare a state of emergency, at which point the Federal Emergency Management Agency would exercise its secretive real power to allow the White House to suspend constitutional government upon declaration of a national emergency and all government, all federal agencies, would come under the power of FEMA.
Shortly after Kurtzweil revealed this information to Mulder and the Syndicate was subsequently alarmed to discover that the alien virus had the ability of causing the gestation of a long-clawed alien inside a human host, Conrad Strughold told the Well-Manicured Man - at a Syndicate meeting in London, England - that the group had been forced to reassess their role in colonization due to their recent discovery and that the geometry of mass infection presented certain conceptual re-evaluations for the group regarding their place in the aliens' colonization. The Well-Manicured Man argued that the situation was not colonization but "spontaneous repopulation". He passionately discussed with Strughold how the group should best proceed, worried that the Syndicate would learn that humans were "nothing more than digestives for the creation of a new race of alien lifeforms", even though Strughold insisted that the group continue cooperating with the aliens while playing for time to continue working on their vaccine.
Privately, the Well-Manicured Man later explained to Mulder how the aliens who had not left Earth prehistorically had been waiting to be reconstituted, using humans as hosts, when colonization took place or shortly before it. The Well-Manicured also told Mulder that, until their recent discovery, the Syndicate had believed the virus would simply control humanity, making humans a slave race and that William Mulder had not only allowed his own daughter to be taken to a cloning facility in the hope that she would survive but had also hoped his son would fight the future. The Well-Manicured Man warned Fox Mulder that his Syndicate colleagues would stop at nothing to clear the way for what they believed was their stake in the inevitable future and implied that this fact had been the reason he had recently followed orders to kill Kurtzweil.
Soon after the Well-Manicured Man was subsequently killed, the Cigarette Smoking Man visited Strughold in Tunisia, worried that Mulder was newly reinvested in his quest to uncover the truth, but Strughold told the visitor that one man alone could not fight the future. (The X-Files Movie)
Mulder subsequently presented a report to the FBI's OPR that cited global domination plans by vicious, long-clawed spacelings – a vague, omnibus account that Assistant Director J. Maslin characterized, during an OPR hearing with Mulder, as "very pie-in-the-sky." Moments later, AD Maslin struggled to make sense of the report, asking Mulder if she was correct in her interpretations that the plot was for the spacelings to take over the planet, aided by a group of men on Earth, and that bees whose sting transmitted a virus would transport the virus from genetically altered pollen that was being grown in the desert by the men. Mulder not only implied that AD Maslin had indeed understood the colonization plot but also declared that he would uncover evidence to prove his claims. (TXF: "The Beginning")
In 1999, after the aliens rebels killed a group of doctors working on Cassandra Spender - the former wife of the Cigarette Smoking Man - but left Cassandra alive, she explained to Agents Mulder and Scully, when they came to visit her in hospital, that she herself had discovered that aliens were at Earth to wipe humans off the planet and were taking over the universe, infecting all other life-forms with the alien virus.
In response to a suggestion - made at a subsequent Syndicate meeting by an alien rebel who had infiltrated the group by disguising himself as a Syndicate member - that the group could join the alien rebels' resistance, Alex Krycek argued, at the same Syndicate meeting, that collaboration had allowed the group to not only prepare but to also stall colonization, that the group's imminent development of a human/alien hybrid alone ensured their survival and that their vaccine was yet another method they had developed to combat the aliens and fight the future.
Shortly after Krycek killed this alien impostor, Mulder described the Syndicate to his FBI superior, Assistant Director Walter Skinner, mentioning that they had been attempting to "develop alien/human hybrids that [would] survive the viral apocalypse when aliens [would] colonize the Earth."
Around the same time that Mulder told Skinner about the Syndicate, the Cigarette Smoking Man recounted to Diana Fowley that his group had had "a perfect conspiracy" with a race of "aliens who were coming to reclaim this planet and to destroy all human life" and that it had been the Syndicate's job to "secretly prepare the way for their invasion, to create for them a slave race of human/alien hybrids." The CSM believed that these plans, which he described as good and right ones, would have worked, had a rebel alien race not come to destroy them. He also blamed the failure of the plans on his betrayal by Jeffrey Spender, a son he had had with Cassandra Spender.
Shortly after she escaped from her hospital room, Cassandra went to Mulder's apartment, where both Mulder and Scully were, and desperately pleaded that Mulder kill her, implying a warning that – if he did not do so – colonization would start with no way to stop it. (TXF: "Two Fathers") Mulder initially acted on her demands, aiming his gun at her, but eventually decided against it and Cassandra was instead transported to Fort Marlene, where she was subsequently confined to a medical room. (TXF: "Two Fathers", "One Son") She would later try to consecutively convince both Jeffrey Spender and his father to allow her to escape – warning Jeffrey that everyone would die, otherwise – but her warnings of impending doom were ignored by both men.
Soon after she was transported to Fort Marlene, another Syndicate meeting was held at which the Third Elder stated his belief that the reason the alien rebels had kept Cassandra Spender alive when they had previously attacked was because they wanted to destroy the humans and knew that colonization would begin when the aliens learned of Cassandra's existence. Even though the Fourth Elder voiced his opinion that they consequently had to destroy Cassandra, the Cigarette Smoking Man told the others to let colonization begin and to turn Cassandra Spender over to the aliens, so that the Syndicate could save themselves. The Fourth Elder then recounted how William Mulder had opposed the Syndicate's option of allowing colonization but the Cigarette Smoking Man argued that William Mulder had sacrificed his daughter because he had known that the particular day which the group now faced would come. The Cigarette Smoking Man then implied his belief that letting colonization begin was the only choice the group had, if they wanted to see their families survive and see those whom they had sacrificed returned to them.
At Fort Marlene, Marita Covarrubias, a Syndicate test subject who had been infected with the alien "black oil" virus during the secret development of the vaccine against it, told Mulder that not only had Cassandra Spender been part of a hybrid program that had been going on for twenty-five years but also that colonization of the planet would begin, with no stopping it, if Cassandra was the first successful alien/human hybrid - as Mulder believed - and the aliens learned a hybrid existed.
Moments after finding the CSM visiting Diana Fowley at her home within the Watergate Apartments, Mulder angrily implied, all the while holding the CSM at gunpoint, that he was disgusted by the CSM's attempt, using innocent women, to save his "own sorry ass, when they finally come knocking." The CSM recounted to Mulder the origins of the Syndicate's alliance with the aliens and the methods the group had arranged in their attempt to survive colonization. Even though the CSM claimed that his group had forestalled an alien invasion and saved billions of lives, Mulder argued that the Syndicate had only managed to postpone the aforementioned invasion and he mistakenly believed that the group had put billions of lives on hold so that the Syndicate members alone could survive the invasion. The CSM tried to convince Mulder into realizing that the Syndicate's effort to create a race of human/alien hybrids had been to ensure that Mulder would also survive, and live to see his sister, mentioning that, after he himself handed Cassandra Spender - the first successful specimen of these human/alien hybrids - over to the aliens, there would be a sequence of events in which a state of emergency would be declared, due to a massive outbreak of the alien virus delivered by bees, and the takeover would then begin.
The Syndicate then began to make final preparations before colonization could begin. By the time of this conversation or shortly after it, the Syndicate had permanently abandoned their offices - on New York City's East 46th Street - and headed to West Virginia. Jeffrey Spender discovered this, after he went to the offices, where, additionally, Krycek told him that the Syndicate members, with the exception of the CSM (who had gone to prepare Cassandra Spender), would be transported by the alien colonists and begin medical preparations to receive the hybrid genes. The Syndicate also permanently cleared out of Fort Marlene, leaving only a heavily infected Marita Covarrubias behind, as Jeffrey Spender also found, and transported Cassandra Spender by train car to the Potomac Yards at El Rico Air Force Base, from where the Syndicate's family members had mostly been taken by the aliens in 1973. Agents Mulder and Scully, warned by Jeffrey Spender regarding his mother's transportation, shot at the train carrying Cassandra and tried to block the vehicle's path with their own car, in an unsuccessful final attempt to prevent the Syndicate from bringing on the sequence of events that would lead to colonization.
However, the Syndicate had been waiting for Cassandra and the CSM to arrive before sending their communication to the aliens and, upon the CSM's delayed arrival with Cassandra, he noticed that the gathered group did not include Krycek, who meanwhile discovered, at Fort Marlene, that the faceless alien rebels had stolen the alien fetus from cold storage and were consequently about to win. Indeed, although no communication was sent by the Syndicate, they were surrounded by the faceless aliens, as the CSM and Diana Fowley fled the area in a car, and were subsequently burned to death. Concerning the apparent destruction of the Syndicate, Agent Mulder remarked, "The future is here and all bets are off." (TXF: "One Son")
After Mulder came across a photograph of Arthur Dales with an Alien Bounty Hunter in 1947, he visited Dales' apartment in an effort to learn more about the image and, at one point, Mulder asked Dales why he and his brother (who was a former Special Agent with the FBI and had spent many years investigating the X-files) had not told anyone about the bounty hunter and plans for colonization, if - over the past fifty years - they had really known about both the alien and the plans. In response, Dales doubted that anyone would have believed him or his brother and stated that Mulder had not been "ripe", although Mulder disputed the latter statement. (TXF: "The Unnatural")
The Syndicate's destruction did not put a stop to the plans for colonization. (TXF: "One Son", "Biogenesis", et al.) The CSM later attended a business meeting at which one man talked about "final preparations for mass destruction on a scale that can only be imagined." After another man asked what they could do to stop it, the first man who had spoken replied, "There appears to be nothing we can do to prevent it. It becomes a question of managing the crisis. Otherwise, we are facing annihilation ourselves." (TXF: "Biogenesis")
Agent Scully meanwhile discovered the possibility of another link between the aliens and an apocalyptic future, when she learned, while in West Africa, that a spacecraft that had recently been found off the coast was believed to be possibly of alien origin and carried symbols on its hull that were translated as being, amongst other things, a passage from the Koran - Quyama, the day of final judgement. (TXF: "The Sixth Extinction")
A rubbing from these same markings had already influenced Mulder to develop a brain abnormality. (TXF: "Biogenesis") Shortly after Scully's discovery, Mulder experienced a dream reality, while the CSM secretly transported his body to a Syndicate medical facility in the knowledge that Mulder was immune to the coming viral apocalypse due to the fact that he was now an alien/human hybrid. As the CSM made an attempt to transfer hybridized genetic data from Mulder to himself, Mulder's dream culminated in him – now aged, frail and dying – being told by the CSM that they were the last humans alive and being shown by the CSM that essentially the end of the world, the final stages of alien colonization, was taking place outside his window. Mulder subsequently made an escape from both this dream state and the Syndicate facility where he had been taken in reality; both of his escape efforts were inspired by Scully who, in his vision, implied that the devil was outside and rhetorically asked Mulder – in response to him claiming that there had been no aliens – whether he had looked outside. (TXF: "The Sixth Extinction II: Amor Fati")
A report contained information, by 2000, about "A conspiracy of men who cooperated with alien beings to create human/alien hybrids, so we could all become slaves of an alien invasion" and this quote was disdainfully read, in that year, to Agent Scully by Special Agent Chesty Short, an FBI auditor, while he was evaluating Scully's and Mulder's work on the X-files. The CSM, now wheelchair-bound, recruited Krycek and a seemingly fully recovered Marita Covarrubias in an attempt to find a crashed UFO in the woods of Bellefleur, Oregon in an effort to rebuild the Project, telling Marita - when she asked him to confirm her belief that aliens were coming to the planet - that they were only coming back. The CSM also commented to Krycek, "As you do to Mulder and to me... you do to all of mankind, Alex", after Krycek consulted Mulder on the UFO's presence (leading to Mulder's abduction) and moments before Krycek pushed the CSM (in his wheelchair) down a flight of stairs. (TXF: "Requiem")
Prior to the Millennium, a doomsday cult in Idaho, led by Travis Clayton Moberly (who went by the name Absalom), believed that aliens would take over the world at the Millennium but, when they didn't, the cult's leader was disgraced and fled the area, escaping a shoot-out there. (TXF: "This is Not Happening")
Special Agent Monica Reyes told Special Agent John Doggett, in 2001, about the doomsday cult who had believed that aliens would take over the world at the Millennium. Absalom (the cult's former leader) claimed, while being interrogated by Scully and Doggett, that he had been right in his prediction of an alien invasion at the Millennium as evidenced, according to him, by the fact that it was since then that injured alien abductees had been being dropped by UFOs in a field in Helena, Montana. (TXF: "This is Not Happening")
About three months later, Absalom - now imprisoned at the Federal Correctional Facility in Perkey, West Virginia - told Doggett that, as part of a big alien takeover of planet Earth, the abductees were being returned, left for dead and would have been (if he and Jeremiah Smith had not intervened and healed them) resurrected as aliens. At the US Naval Hospital in Annapolis, Maryland, Doggett relayed news of this claim to Scully, soon after Absalom had made it, because it helped to explain the conditions of Billy Miles and Mulder, who were both recently returned abductees. (TXF "DeadAlive")
Later that year, Howard Salt – a US Census worker and multiple alien abductee who had been one of Absalom's disciples – accidentally shot himself to death with his own weapon after climbing over the perimeter fence surrounding the White House, desperate to tell the President that aliens were taking over the United States and carrying a computer diskette bearing the words "fight the future". News of this incident was smuggled to Absalom, hidden inside a book titled The Coming Apocalypse. Absalom subsequently escaped from confinement, leaving the words "fight the future" on a wall of his cell; AD Skinner soon thereafter told a roomful of FBI agents, while briefing them on Absalom's escape, that – although the FBI did not know the meaning of the three words – Absalom had "claimed to have knowledge of an alien invasion".
Despite Absalom's suspicion that Salt had been killed for what he knew and his fear that he himself would be killed by the same forces, he set out to show Agent Doggett that the invasion had already begun and that the aliens were already present, so that the skeptical Doggett (who Absalom referred to as "Doubting Thomas") could spread this news. When asked by Doggett to clarify what invasion he was referring to, Absalom cryptically replied, "Certain men have gone out among you and have withdrawn the inhabitants of their city saying, 'Let us go, and serve other gods that ye have not known.'" Doggett was still unclear about his kidnapper's intentions and Absalom himself admitted that his statement had been cryptic, suggesting that what he had referred to was information that had been "kept secret from the world."
While Absalom held Doggett hostage, the two men managed to break into the Federal Statistics Center in Crystal City, Virginia, where Absalom cryptically insisted that proof that aliens were already among the human population was hidden within a certain room where the government compiled all the available data from the US Census. Absalom was killed by a squad of well-armed men outside this locked room, however.
As Mulder discovered by later breaking into the facility himself, the password for the heavily secured database in this room was "fight the future" and the database contained names of people who had a certain genetic profile and who had been the subjects of tracking by the federal government, using the US Census. Mulder believed that both Howard Salt and Absalom had known about this data and that the database constituted proof that the people whose names were included had been targeted, due to their genetic profiles, for abduction and replacement by alien facsimiles. Although Mulder's attempt to widely release this information was unsuccessful, the source of the password he had used to access the database was Knowle Rohrer, who was one of the alien facsimiles himself but was acting as an informant to Agent Doggett. (TXF: "Three Words")
When Mulder became insistent that the death of an oil worker (Simon de la Cruz) was due to exposure to the black oil virus, Doggett mentioned – while revealing to Mulder what he himself knew of Mulder's beliefs about the virus – that the alien substance was "part of an alien conspiracy to colonize the planet." While aboard the rig himself, Mulder came to suspect that a new oil field, which was being pumped by the Galpex Orpheus (the oil rig on which Simon de la Cruz had been working, at the time of his death) contained many billions of barrels of the virus, waiting to infect the ninety percent of the planet's population who were dependent on oil.
Furthermore, Diego Garza – a friend of Simon de la Cruz who, like him, had a rare genetic immunity to the virus and was the only member of the crew who had not been infected with the black oil – feared that men in flying saucers were coming to get him. He died soon after expressing these fears to Doggett, however, and the rig exploded shortly after Garza's death, as both Mulder and Doggett made a hasty escape from the doomed rig.
Following the agents' return to FBI Headquarters, Doggett received news that Galpex had lost the right to drill the entire Texas oil province where the Orpheus had been pumping oil; Mulder was of the opinion that not only should the oil remain where it was but that Doggett should do everything he could to ensure the oil stayed in that location, and Mulder told him as much. (TXF: "Vienen")
Later that year, Krycek brought several claims to Mulder, Scully, Doggett and Skinner, including his revelation that Billy Miles and alien replicants of his ilk wanted "to knock out any and all attempts by us to survive the final days, when they come back to retake the planet." (TXF: "Essence") Krycek later also claimed to Mulder, Doggett and Skinner that these aliens were newly created to aid in the planet's repopulation, which the birth of Scully's as-yet unborn baby was apparently a threat to. Shortly after Krycek made these claims, however, he was shot to death by Skinner, and Scully gave birth to her son, William, while unharmed by an observing group of alien replicants whose presence at the birth proved the claims that there were many of these aliens. (TXF: "Existence")
In 2002. after one of the alien replicants and Special Agent Robert Comer consecutively insisted to Scully that her son had to die but were both defeated before they were able to explain further, Scully and Agent Monica Reyes were told by a hospitalized Agent Comer that the followers of a cult – which he had been assigned to investigate, undercover, and had recently kidnapped baby William – believed that an alien race would "rule the world". (TXF: "Trust No 1", "Provenance", "Providence")
Agent Comer continued to reveal a prophecy that explained why he had made an attempt on baby William's life. Reportedly, the cult's leader, Zeke Josepho, had said that God had spoken to him of a miracle child, a future savior coveted by forces of good and evil, and Josepho believed that this child was actually Scully's son. According to Agent Comer, Josepho believed that William would follow in his father's paths, making an attempt to stop the aliens' return, unless his father was to be killed. Josepho, his cult and even Agent Comer himself believed that Mulder was already dead and Comer warned Scully that, if William did not die, "all of mankind [would] perish from Earth." Reyes later doubted this prophecy, when she privately spoke to Scully, but Josepho, in a private meeting with Scully, claimed that, although he thought it was highly incredible, her son would lead the alien race of replicants and had been "put here to lead." Subsequently, Josepho's cult was effectively destroyed and Scully was finally reunited with William. (TXF: "Providence")
Later that year, the baby's partly-alien biology was normalized by a facially disfigured Jeffrey Spender (using an intravenous dose of magnetite) and, while in a questioning room alone with Scully, he recounted that his father, the Cigarette Smoking Man, had – following his failure as a conspirator to control alien colonization – wanted nothing more than to also see the world fail. Eager to understand the significance of what Spender had said in relation to what he had done to William, Scully asked him if he had prevented alien colonization by injecting William with magnetite. Spender did not directly answer Scully's question but claimed that her son was "the one thing the aliens need" and that he himself had thereby taken revenge on his own father by taking William away from the aliens. Despite Scully's hopes that this meant the aliens would leave William alone from now on, Jeffrey Spender warned her that the aliens would always know what William had been and would never accept what he now was. Spender also implied that, if Scully failed to protect her son, William would or might be subjected to the same disfiguring procedure that he himself had been forced to undergo. As a result of her fears about William's future, Scully adopted her son, shortly after her conversation with Spender. (TXF: "William")
After Mulder sneaked into the Mount Weather complex in Bluemont, Virginia later in 2002, he managed to secretly gain access to a computer system that held information about plans for the forthcoming colonization (including the date of the final alien invasion) and displayed this information on a transparent screen but, soon thereafter, the alien Knowle Rohrer destroyed the screen and Mulder was captured. A trial was arranged for Mulder, due to the fact that he had apparently killed Knowle Rohrer (who was, due to his alien essence, virtually invincible, other than due to exposure to magnetite), and – shortly before the trial began – Mulder had a private conversation with Scully in which he revealed that he had been looking for the truth in New Mexico but refused to admit what he had discovered at Mount Weather, even though Scully could intuit that he had learned something in his search for the truth.
Scully was the first witness to be called during his trial and, as part of her testimony, she detailed the government's discovery of the colonization plan. In response to FBI Deputy Director Kersh asking if this account was leading the trial anywhere, Mulder spoke up to casually answer, "Yeah, the destruction of mankind", prompting a warning from Kersh. Scully continued by stating that the government had kept the aliens' colonization plan "a dark secret" to avoid wild panic.
Scully later tried to persuade Mulder to take the stand himself and expose whatever he was withholding, but he declined and told her that he couldn't do as she asked. At one point soon thereafter, Mulder was visited in his cell by the ghost of X, who accused him of being too afraid to speak a certain truth and claimed that that was because Mulder knew that speaking of it would be futile, but Mulder refuted these claims and instead argued that the reason he would not speak of that particular truth was that he refused to accept it. Moments after it was revealed that one of the judges was an alien replacement, a disruptive Mulder accused the judges of being afraid of the truth that he knew.
Later in the trial, the prosecutor, Special Agent Kallenbrunner (having heard Scully state that the conspirators had been working to develop hybrids for the aliens to use as slaves), asked Reyes whether the government program to create alien babies, a program that had involved Scully, was also for the creation of a slave race, and Reyes confirmed that it had been.
After Mulder was given the death sentence but escaped from confinement with the help of his associates, he was desperate to know more about the truth of alien colonization and whether he could change it so he headed back to New Mexico with Scully, having been given a key for Mount Weather from a rumored wise man who lived in New Mexico. The "wise man" turned out to be the Cigarette Smoking Man, who criticized Mulder for being too afraid to reveal the truth regarding colonization and told him that testifying what he had learned would have saved his life. The CSM claimed that the magnetite-rich area where he now lived was the final refuge from the aliens who were meanwhile insidiously taking power and, despite Mulder's objections, he insisted on telling Scully about colonization. He told her that the story of the future event had scared every president since Truman and informed her of the same date that Mulder had learned, adding that Mount Weather was where the secret government of the US would be hiding during the event.
The CSM was killed soon thereafter and – at night in a motel in Roswell, New Mexico – Mulder reminded Scully that the CSM had said that the date was not only set but was also unchangeable. In turn, Scully reminded Mulder that he had refused to tell her what he had learned about colonization. She believed that he had withheld that information because he had not wanted to accept defeat, rather than because he had been afraid or broken, but Mulder clarified that he had been afraid of how the knowledge would effect her, having specifically feared that it would crush her spirit. Scully asked Mulder why she would accept defeat, implying that she would not, and the two fugitives ultimately hoped that there was still hope for the future. (TXF: "The Truth")
The Syndicate had learned, by 1998, that the final stages before colonization would begin were scheduled, according to the aliens' timetable, approximately fifteen years after 1998. (TXF: "Patient X") However,according to the cigeratte smoking man the date of colonization is set to be the 22nd of December 2012 (The Truth)
The teaser of "One Son" features a voice-over that is said by Mulder actor David Duchovny and concerns the Syndicate's role in colonization, firstly pertaining to the subject of William Mulder and the Cigarette Smoking Man. Visual footage accompanying the voice-over shows first a burning black-and-white photograph of the two men and then the Syndicate welcoming the aliens at El Rico Air Force Base in 1973. The voice-over states:
- "Two men, young, idealistic -- the fine product of a generation hardened by 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 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."
- During preproduction of Season 3 finale "Talitha Cumi", writer Chris Carter at one point decided to remove the word "colonization" from the scripted version of the scene in which Mulder asks X if he is talking about that event. Carter initially thought the inclusion of this term was too revealing but he later reversed his own decision regarding this issue, causing viewers to ponder the meaning of the term during the interim between Seasons 3 and 4 of The X-Files. (Trust No One: The Official Third Season Guide to The X-Files)
- The aliens are occasionally referred to as "Colonists" due to their plans for colonization.
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