Well. The X-Files came back for a miniseries, or season 10, whatever you want to call it. But instead of wrapping up their mythology about alien invasion and a government conspiracy they kind of ended things on a cliffhanger. So I guess we’re getting more X-Files. The mythology used to be the show’s main selling point but it’s become fairly convoluted. It was moving forward at a good pace all the way through season 6, seemingly entering its final act for season 7. But then, even though star David Duchovny opted to leave (he still guest starred in a few episodes throughout season 8 and the finale in 9), producer Chris Carter opted to keep the show going. And the mythology went kind of off the rails. The show never really had a planned end, so questions kept getting asked instead of any getting answered. Regardless, it CAN be summarized. So that’s exactly what we have done.
We have two parts:
- One is a smaller summary about the overall conspiracy
- The second breaks down what Mulder and Scully do, season by season
The Overall Conspiracy
The alien Colonists arrived on Earth in prehistoric times with plans to later invade and wipe out humanity. The Colonists were patient and preserved themselves underground as an intelligent pathogen later known as the Black Oil. It is an evolved virus that could infect humans and take control of their bodies. Somehow the Mayans discovered them at some point and predicted they would invade Earth in 2012.
Humanity initially discovers the existence of the Colonist invasion when a Colonist UFO crash lands in 1947 Roswell, New Mexico. These aliens look like the traditional “grey” aliens with large black eyes. The State Department is called in and begins studying alien biology and the spacecraft itself, working to create their own Alien Replica Vehicles (ARVs) based on the technology. They are also able to access the data banks on the alien craft and discover the plan to invade Earth. A secret organization forms within the state department which includes C.G.B. Spender (commonly referred to as the Cigarette Smoking Man, or CSM) and Bill Mulder. It becomes known as the Syndicate, which grew to have its own secret black ops team within the government. The Syndicate believes the Colonists plan to take control of human bodies and contact them to pretend to cooperate. Secretly, they were buying time.
The Colonists and the Syndicate agree on an exchange: everyone in the Syndicate gives over one of their children or a loved ones to to be experimented on in exchange for an alien fetus. The Syndicate plans to use the fetus to create a human/alien hybrid that would be immune to the Black Oil, believing the aliens intend to take over humanity that way. Bill Mulder decided to give up his son, Fox but the aliens insist on taking his 8-year old daughter, Samantha, because they need a young girl for their experiments. Fox Mulder witnesses his sister being abducted at 12 years old.
The government uses Nazi research to clone multiple Samanthas. Some were mindless and some were drones that were duplicates of 8-year old Samantha. They were ultimately all killed by an Alien Bounty Hunter because the Colonists were not comfortable with the Syndicates experiments. The Samantha drones worked on a bee farm which the Colonists were creating to disseminate the Black Oil virus. These bees were a modified, aggressive Africanized bee who fed on corn pollen which was genetically engineered to carry the virus. The aliens experimented on Samantha and returned her only to then be subject to painfully invasive hybrid experiments overseen by CSM. She ultimately ran away and was granted a peaceful death by supernatural creatures known as Walk-Ins who save children that are doomed to live lives of pain.
When Fox Mulder grows up he becomes an FBI agent and investigates strange cases, known as X-Files. His goal is to ultimately find his abducted and still-missing sister. The Syndicate pressures the FBI into assigning him a partner, Dana Scully, who will ostensibly use her medical background to debunk and discredit Mulder’s work. When they instead form a solid partnership, Scully is abducted by the Syndicate. Her ova are taken for hybrid experiments. They grow a biological daughter, Emily, as an alien hybrid but it dies prematurely. The first successful hybrid is CSM’s ex-wife, Cassandra Spender. The Syndicate hands Cassandra over to the Colonists, with the intent to trigger an early Colonization they believe they are ready for, when everyone present, except for CSM, is destroyed by alien rebels who oppose the Colonization. These aliens look like humans with plastic faces – no eyes, nose or mouth holes.
With the Syndicate and alien hybrid destroyed, the Colonists send in super-soldiers (aliens who look human created with a new, mutated version of the Black Oil). This Black Oil instead gestates aliens and kills the human host, which was the Colonists ultimate plan all along. Mulder is abducted by the aliens and nearly turned into a super-soldier but is rescued. Mulder and Scully have a child, William, the first organically born super-soldier, although the details of his conception are never fully explained, especially since Scully’s abduction supposedly made her infertile. The super-soldier aliens infiltrate the U.S. government, secretly blocking attempt to survive colonization, still planned for the future.
CSM later implements the Spartan Virus, which has been latent in all American citizens given a smallpox immunization. Only a select few, chosen by CSM, have alien DNA implanted to give them immunity to the virus. The virus compromises everyone’s immune system but Scully is able to engineer a cure based on alien DNA in herself. Mulder is too sick to be cured and Scully realizes the only way to save him is with stem cells from their son, William, who they gave up for adoption 14 years ago.
Mulder and Scully’s Investigations
FBI Special Agent Fox Mulder discovers the FBI’s X-Files—unexplained cases which may be paranormal in origin, in 1990 and begins working on them. In 1992, the agency appoints Dana Scully as his partner. With her medical degree, his superiors hope to debunk and discredit his work. Their first case together involves a potential alien abduction in Oregon but all their evidence mysteriously is burnt. Later, Mulder meets a secretive informant known as Deep Throat, who gives the team hints towards uncovering a government conspiracy. They also get help from a trio of conspiracy theorists who call themselves The Lone Gunmen. When Deep Throat points the agents to a government cloning program, the Syndicate has Deep Throat killed and the X-Files closed.
Mulder investigates possible extraterrestrial contact in Puerto Rico, when he learns that the SETI (Search for Extra Terrestrial Life) program has been shut down. He is given a new partner, Alex Krycek, who unbeknownst to him reports to The Syndicate. Mulder also meets a new informant, X, who used to work with Deep Throat, but is much more cautious about being discovered. Scully teaches at the FBI Academy but is kidnapped by a deranged multiple alien abductee, Duane Barry. Barry takes Scully to a hilltop where she is then abducted, seemingly by aliens. Mulder and Scully’s superior, Assistant Director Walter Skinner, uses this as leverage to reopen the X-Files. Scully is later found comatose at a hospital with no details on how she arrived. X offers Mulder information on how he can get revenge on Scully’s abductors but he opts to stay by her bedside. Again working together, Mulder and Scully cross paths with a shape-shifting Alien Bounty Hunter who is killing off clones. Mulder is called by his father because his adult sister, Samantha, has returned. She claims to be being hunted by the Alien Bounty Hunter. She is killed by the bounty hunter but Mulder and Scully learn that she was a clone, created in an attempt to make a human-alien hybrid.
The Lone Gunmen contact Mulder and Scully about a successful hack of the United States Department of Defense computer system by their friend, Kenneth Soona. Kenneth gives Mulder the info on a digital cassette, which is in Navajo. Kenneth is assassinated at the direction of CSM who is hunting down the tape. He also visits Bill Mulder and it becomes clear they know one another. Krycek murders Bill Mulder just before he can tell Fox everything about the conspiracy that he knows. Krycek escapes. Scully proves that Mulder’s gun did not shoot his father and also realizes that Mulder’s tap water has been drugged, making him agitated, in an attempt to frame Mulder for his father’s murder. She puts Mulder in touch with Albert Hosteen, a Navajo man capable of translating the files, and which contain information about Scully’s abduction. Hosteen introduces Mulder to his grandson, who takes Mulder to a buried boxcar in the New Mexico desert. Inside, Mulder finds a pile of dead creatures that look alien and have smallpox immunization scars on their arms. CSM calls Mulder and is able to find where he is, showing up in a helicopter with black ops soldiers who blow up the train car with Mulder seemingly inside.
Mulder is able to get out of the traincar and hide under some rocks when the soldiers showed up. He is still wounded but is found and nursed back to health by Hosteen. Meanwhile, Scully investigates a lead on how the smallpox immunization program could have been involved, leading to the discovery of a Nazi scientist working for the U.S. government to create alien-human hybrids. Scully’s investigation brings undue attention from The Syndicate who order to have her assassinated but the assassins mistake her sister, Melissa, for her and kill her. Mulder and Scully later investigate evidence of an alien autopsy. It brings Scully to a group of women who claim to also have been abducted, like Scully, all have a tiny implant like her, and they all have cancer. Mulder ultimately tracks down the train car and jumps aboard it. He is attacked inside the train by a Syndicate assassin who is guarding a human-alien hybrid. Meanwhile, X has told Scully to investigate her implant for answers. She ultimately meets the First Elder, a high ranking Syndicate member who claims she was abducted and experimented on a similar train car and that the alien story is a smokescreen. X shows up and saves Mulder but the train, hybrid and assassin are all blown up.
Later, a French salvage ship raises a World War II-era plane from the sea floor. The entire crew is immediately struck down with massive radiation burns except for one who has been infected with a parasitic Black Oil that was on the submarine. The Black Oil controls the man and moves from hosts to host, ultimately getting to Hong Kong where a middleman is selling government secrets and Mulder is pursuing. The woman has the digital tape but Krycek has broken into her office to steal it and gets away. Mulder later catches up to him at an airport and Krycek offers him the tape in exchange for his life. As Krycek cleans himself up in the bathroom, the alien-controlled host moves to possess Krycek. Skinner is confronted by a Syndicate member, the Gray Haired Man, and told to stop investigating Melissa Scully’s death. When Skinner refuses, he is later shot by a Syndicate assassin but he survives. Skinner and Scully identify his would-be assassin as the same man who killed Melissa. Mulder finds the digital tape case is empty. Krycek hands the tape over to CSM in exchange for the location of a hidden UFO in a missile silo. Mulder finds a phone number on the case and gets in touch with a Syndicate member, the Well-Manicured Man. He warns Mulder that anyone can be got to which leads Mulder to warn Scully to protect Skinner. Scully is able to apprehend the assassin, though he is later killed in prison. Meanwhile, Krycek coughs up the Black Oil into the UFO. Krycek is left trapped in a silo room.
Mulder’s mother meets with CSM and later suffers a stroke. Meanwhile, a mysterious man named Jeremiah Smith has healed a man that was shot and is interrogated by the police, then released. The man works at Social Security Administration and is taken by CSM. Mulder visits his mother and then her house where X is waiting for him and lets him know his mother knows CSM. Mulder then finds a stiletto, the weapon that the Alien Bounty Hunter uses, hidden in his mother’s house. CSM interrogates Smith who is revealed to be a shapeshifting alien. When Mulder goes to the SSA to talk to Smith, he runs away into the crowd and shapeshifts. He later goes to kill the original Smith only to see that he’s escaped the CSM’s cell. Mulder visits his mother at the hospital and encounters CSM. CSM says he spoke with Mulder’s mother about the whereabouts of Samantha. Mulder then encounters X in the hospital elevator and X demands the stilleto but Mulder refuses and they grapple to a standstill. Scully finds there are multiple Jeremiah Smiths at SSA offices around the country. Mulder and Scully meet the original, “good” Smith with a plan to get him to Mulder’s mother when the alien bounty hunter shows up.
Mulder is able to sneak behind the Alien Bounty Hunter and stab him with the stilleto. Mulder and Smith escape on a boat while Scully stays behind. The Alien Bounty Hunter wakes up and threatens Scully but realizes she doesn’t know where Mulder’s gone. Smith convinces Mulder to go to Alberta, Canada with him where they will find Samantha. Meanwhile, the First Elder and CSM realize they have a leak if Mulder learned about CSM’s meeting with Mrs. Mulder and set a trap to find their leak. The bounty hunter listens to Scully’s call to Mulder and begins tracking him. Skinner tells Scully all the other Smiths have disappeared. Scully contacts X to help decipher the info that the Smiths were collecting and he tells her to investigate the smallpox program. Smith takes Mulder to a field where corn is being tended by mute clones of 8-year old Samantha. The bounty hunter shows up but they are able to crush him under a massive beehive. Mulder takes one of the clones back to D.C. But the bounty hunter catches up to the trio and crashes into their car, taking the clone and chasing Smith. Skinner and Scully realize the Smiths were examining a cataloging of everyone from the smallpox program. X is led to Mulder’s apartment and killed by Syndicate assassins. As he dies, he leaves clues to direct Mulder to a new contact – Marita Covarrubias, the assistant to the Special Representative of the Secretary General of the United Nations. She tells Mulder that the fields have been abandoned. Meanwhile, CSM orders the Alien Bounty Hunter to heal Mrs. Mulder because otherwise, Mulder would have nothing to lose and be more dangerous.
Later, Krycek alerts Mulder and Scully to a terrorist event that they stop. Terrorists had released him from the silo and Krycek uses them to get in touch with Mulder, telling him he’s ready to turn on the Syndicate. He alerts them to a courier who they apprehend. He’s carrying an old meteorite fragment that an FBI scientist inadvertently releases Black Oil from and is put into a coma. Marita tells Mulder the rock came from Russia. He reluctantly takes Krycek with him to the site in Russia because Krycek is fluent in the language. They come across a slave labor camp and are imprisoned in the gulag. Mulder has a Black Oil vaccination tested on him that works. Mulder and Krycek escape but are separated. Krycek encounters men missing left arms and they forcibly chop his off to prevent themselves from being used in vaccination tests. A former KGB assassin is reactivated and sent to America where he kills a Syndicate scientist that was also developing a vaccination of their own. Mulder returns to D.C. but the assassin returns to Russia to report to Krycek.
Scully learns she has cancer, like the other women abductees she met. Scully and Mulder are told by Kurt Crawford, a man in the abductee network, that all of the women she met are dead from cancer. Scully begins chemotherapy while Mulder and Crawford (who is actually an alien shapeshifter that killed the original Crawford) look into hospital databases and find Scully’s name in a fertility clinic database. Mulder goes there and finds multiple Crawford clones, the male equivalent of the Samantha drones. They explain that they were birthed from ova taken by the female abductees and show Mulder to Scully’s harvested ova which he takes. The Gray Haired Man shows up and kills all the Crawford clones after Mulder has left. Meanwhile, Mulder had asked Skinner to arrange a meeting with CSM to find a cure for Scully, believing the cancer comes from her abduction. Skinner advises Mulder not to do that but secretly brokers such a deal himself.
A team of Canadian scientists find ice core samples containing what they believe could be alien DNA and send them to the X-Files team. Scully confirms there is non-terrestrial DNA present. Mulder heads to Canada to investigate while Scully is attacked and has her samples stolen. She tracks the man down and finds he is a Defense Department employee, Michael Kritschgau. He claims he could be killed. Mulder and the scientist find the whole scientific team has been murdered except for one man who hid along with an alien corpse they dug up. While the scientists begin an autopsy, Mulder goes to see Scully. Kritschgau tells them that everything about the alien invasion is a hoax designed to cover up illegal experiments by the government, including Samantha’s abduction. Meanwhile, an assassin kills the Canadian scientists. Kritschgau claims Scully was given cancer just to show Mulder what the secret military industrial conspiracy is capable of and make him believe.
Mulder, in his apartment, has lost faith in his crusade. A call from Kritschgau warns him that he is being targeted and Mulder realizes there is an assassin in the apartment above his. In a struggle, Mulder kills the man and shoots him in the face. It is the same assassin that killed the Canadian scientists. Mulder fakes his suicide to provide a decoy and give him time to infiltrate the Pentagon, looking for a cure to Scully’s cancer. He ultimately finds a secret area that has fake alien bodies and massive filing records on everyone. He finds a small vial with metal in it in Scully’s file and believes it to be a cure. The Lone Gunmen tell Mulder it is only deionized water. Mulder goes to check on Scully but he is brought in by Skinner and an angry Section Chief Blevins who was told by Scully that Mulder had commit suicide. Mulder tells Skinner that a mole inside the FBI gave Scully her cancer. CSM meets with the First Elder and says Mulder could join them with the right encouragement. After Mulder visits Scully at the hospital, CSM meets him and says the chip in the vial of water can cure Scully’s cancer. Meanwhile, an FBI panel interrogates Kritschgau who says he does not actually work for the Department of Defense, just a lobbying firm called Roush. Scully decides, despite the skepticism by her family, to insert the chip. CSM contacts Mulder and meets him at a diner with an adult Samantha, who claims CSM is her actual father but is reluctant to say anything else. CSM says that if Mulder joins him, he will get explanations. Mulder then meets with Blevins who says he has evidence of Skinner withholding evidence from the assassin that Mulder killed. Blevins tells him to finger Skinner as the traitor. Back at the panel, Mulder instead says that Blevins is the traitor. Blevins, shocked, runs back to his office where a senior agent is waiting for him and shoots him dead, masking it as a suicide. Meanwhile, a Syndicate assassin shoots CSM. Skinner later tells Mulder that CSM was shot dead but his body disappeared. He also reveals Blevins was on the Roush payroll, confirming he was being paid by the Syndicate. Scully’s cancer goes into remission.
A rebel alien race, who have no holes on their faces, begin attacking former alien abductees. In Russia, one boy escapes such an attack only to be taken by Krycek, who has his men infect him with the Black Oil. Marita shows up with a UN team and Krycek tells her everything is going to hell. Meanwhile, Mulder attends a lecture at MIT by former abductee Cassandra Spender. Mulder expresses skepticism to her and the professor. Cassandra tells Mulder that the aliens are in a state of upheaval and she will be abducted again. Krycek sews the boy’s eyes and mouth shut so that the Black Oil cannot escape and takes him to the U.S., against his Russian superiors’ orders. Scully meets FBI Agent Jeffrey Spender, who is Cassandra’s son and asks her to keep Mulder away from his mother for fear of ruining Agent Spender’s reputation. Krycek offers the infected boy to the Syndicate in exchange for their information on the vaccine they’ve been working on. Marita also meets with the Syndicate who reveal they were expecting a much later invasion date and are confused by the recent attacks on former abductees. Krycek goes to check on the infected boy but instead the Well Manicured Man is there, waiting for him. Marita has taken the boy and calls Mulder to come over. The boy rips his stitches out and infects Marita. Mulder calls Cassandra to reach Scully but gets Agent Spender instead. Cassandra and Scully are meeting with other abductees on Ruskin Dam when a spaceship shows up. But the happy group begins screaming when two faceless rebel aliens show up.
Mulder rushes there and finds Scully and about 50 other survivors but Cassandra is missing. The Syndicate tests their vaccine on Marita, which doesn’t work yet. The Well Manicured Man talks to Krycek, convinced the Russians have developed a working vaccine. Meanwhile, a rebel alien crashes in West Virginia and is captured by the military. The Well Manicured Man argues to the Syndicate that they should align themselves with the rebels but the other Syndicate members are reluctant and want to test the Russian vaccine first. The Russian vaccine is tested on Marita but appears to have no effect. The First Elder tells the Well Manicured Man that the Syndicate has elected to hand the rebel over to the Colonists and continue with their original plan. Krycek is released and tells Mulder that the rebels are delaying the colonization and they must not allow the rebel to be handed over. Mulder heads to the West Virginia base and witnesses the Alien Bounty Hunter, disguised as a government agent, heading to kill the rebel. Instead, a second rebel arrives and saves the first. Back at FBI headquarters, Agent Spender receives a letter. We cut to a cabin in Canada where the letter is returned, unopened, to the CSM who is still alive and recuperating.
A Russian chess grandmaster is playing in a tournament against an American child prodigy, Gibson. A Syndicate assassin in the rafters aims at Gibson but just as he fires, Gibson casually moves and the assassin kills the Russian player instead. In the course of the investigation, lead by Agent Spender, Mulder interviews Gibson and believes he is telepathic, which allows him to play chess so well. It also means the target was Gibson. Meanwhile, Krycek tracks down CSM and brings him to the Syndicate. The First Elder and Well Manicured Man want his help with Gibson. The shooter is in custody but won’t talk. Mulder wants to offer him immunity in exchange for his testimony and also believes their tests on Gibson prove everything the X-Files is about, and that Gibson has genes that are dormant in most humans. Mulder also thinks he spies CSM and Spender talking in the FBI parking garage. Ultimately, a corrupt guard kills the shooter and Gibson is abducted from a safe house by CSM’s men. CSM turns Gibson over to the Well Manicured Man. The Justice Department, having no evidence, shuts the X-Files down. CSM enters Mulder and Scully’s office, takes Samantha’s folder, and sets the room on fire. On the way out he encounters Agent Spender and reveals that he is his father.
The X-Files: Fight the Future (movie)
Mulder and Scully are on a mission to deal with a terrorist bomb threat and Mulder suspects the government building across the street is the actual target and everything else is a distraction. He finds a bomb but an FBI agent who secretly works for the Syndicate insists on defusing it and evacuating everyone else. Instead, he allows it to explode. Following that a doctor approaches Mulder, claiming he knows about a new strain of the Black Oil in North Texas that has been discovered. It is shown to infect people and allow aliens to gestate inside the host (killing the host) within 96 hours, instead of just controlling the human. The doctor says the bombing was a conspiracy to hide the evidence from the public. Mulder and Scully investigate and find a corn farm in the middle of a desert. Scully is stung by an oil-infected bee, collapses and is abducted by men in black, working for the Syndicate. The Well Manicured Man meets with Mulder and is told where Scully was taken and given a weak vaccine they’ve created. The Well Manicured Man is subsequently assassinated by the CSM, working for the Syndicate. Mulder heads to Antarctica where he finds a massive spaceship buried beneath the ice. Inside is a lab that has been run by CSM and Scully is in stasis in a pod. He frees her and administers the vaccine, curing her and the spaceship leaves. Later, Scully testifies in front of an FBI hearing and reveals the genetically engineered bee, which the Lone Gunmen kept safe. She says the FBI is not currently equipped to investigate such strange cases, which leads to the X-Files being reopened.
While the X-Files have been re-established, Mulder and Scully are denied assignment to it. Instead, they’ve been replaced by Agent Spender and Agent Diana Fowley while Mulder and Scully report to Assistant Director Kersh. A scientist working for Roush gets infected by the Black Oil and gestates an alien that bursts out of him and heads for a nuclear plant in Arizona. The CSM is assigned to track it down by the Syndicate and he kidnaps Gibson to help track it. Gibson escapes the CSM but is captured by another Syndicate member, the Black Haired Man, and taken to the nuclear plant. There, the alien attacks the Black Haired Man but leaves Gibson alone. Scully explains to Mulder that the alien DNA they’ve examined is embedded in every human being but is only active in Gibson. Back at the plant, Gibson witnesses the alien shed its skin to reveal a traditional “Grey” alien.
Skinner, at one point, ends up in the hospital. Mulder and Scully realize he’s been infected with a nanovirus. Unknown to them, Krycek has infected Skinner and can turn the virus on and off, to control them down the road.
In a train car lab, scientists operate on Cassandra Spender and it is revealed she has green blood and can heal wounds instantly. Alien rebels arrive and kill the scientists, leaving Cassandra alive to be found by the FBI. A Syndicate elder is killed by an alien rebel who shape-shifts to take his place. Cassandra tells Mulder and Scully that the aliens move from planet to planet, wiping out indigenous life and colonizing it. She also says there are rebel aliens against this who mutilate their faces to prevent infection from the Black Oil. Meanwhile, Krycek updates the Syndicate on the rebel alien attacks. The disguised alien Elder recommends aligning with the rebels and the CSM seems to notice that that’s a reversal of his previous opinion. Mulder and Scully break into the X-Files and find out that CSM is named C.G.B. Spender and worked with Bill Mulder at the State Department. Meanwhile, Agent Spender is ordered by CSM to kill the Elder who is really an alien. Spender fails but Krycek shows up and finishes the job. Krycek tells Agent Spender that CSM was responsible for Cassandra’s abduction, which upsets Agent Spender. CSM tells Agent Fowley the truth and she agrees to help him, moving forward. Cassandra escapes the hospital and goes to Mulder’s apartment. She begs him to kill her because she is the first successful human-alien hybrid and if the aliens discover this, they will begin Colonization early.
Before Mulder can do anything, Agent Fowley quarantines Mulder, Scully and Cassandra and tells the CDC that Cassandra has a contagious organism. Krycek reports to the Syndicate and indicates the rebel aliens want Cassandra kept alive but the Syndicate decides to hand her over to the colonists and save themselves. Mulder encounters Marita at the CDC site and she explains that the Syndicate has been testing vaccines on her. Mulder encounters CSM and a lot is explained. CSM says Agent Spender has betrayed him. He also elaborates on how the Syndicate had a majority vote to align with the colonists years ago against Bill Mulder’s objections. They each handed over a loved one, including CSM’s ex-wife and later, Samantha, in exchange for an alien fetus. They could create a human-alien hybrid with it and once they did, the aliens would begin colonization, which they will now that Cassandra has become a hybrid. He then tells Mulder where the Syndicate is planning to hand over Cassandra so that Mulder can stop it. A Syndicate surgeon gathers the alien fetus but is killed by an alien rebel. At the base, the alien rebels surround the Syndicate and Cassandra and immolate them all. CSM and Agent Fowley escape. At the FBI headquarters, Agent Spender says he thinks Mulder and Scully could have prevented his mother’s death and recommends they be reassigned to the X-Files. He goes to clear out his office but the CSM is there and he berates him for not being more like Mulder and shoots him in the head.
Mulder and Scully investigate a bizarre rock inscribed with Navajo writing found in Côte d’Ivoire, and the death of the African scientist involved. The rock begins to affect Mulder’s mental health, leading him to turn to Agent Fowley for help. Krycek is revealed to be using the nanotech virus to make Skinner report on the investigation to him, as well as hide some info from Mulder and Scully. Mulder believes the rock could prove that aliens began human life on earth (the panspermia theory) but Scully is determined to disprove the theory and heads to New Mexico to get translation help from Albert Hosteen, who she finds is sick and dying. The rock includes passages from the Bible and a map of the human genome. While Mulder breaks down in a mental institution, Scully journeys to Africa in hopes of finding a cure.
Skinner and Kritschgau try to figure out what the alien rock is. Scully investigates what could be a massive alien ship buried on the coast of Côte d’Ivoire that could prove that aliens made contact with Navajo in the distant past but can’t come up with anything concrete and returns to D.C. Mulder is missing so Scully turns to Agent Fowley who tells her where Mulder is. He took Mulder to a government facility to heal Mulder, revealing that he is Mulder’s biological father. CSM believes alien infection has made Mulder a human-alien hybrid and plans to have part of his brain tissue removed and implanted in him, but the procedure fails to give CSM any abilities. Krycek kills Kritschgau. Scully finds a security card slipped under her door that she tracks to Mulder’s location where she saves him. CSM kills Fowley for betraying him.
Mulder later asks to help an investigation of a little girl. Along the way, he learns about Walk-ins, spirits that protect children doomed to live painful lives. Meanwhile, Mulder’s mother commits suicide because she had developed cancer. While Mulder suspects murder, Scully is able to confirm it was a suicide. In the investigation, Mulder arrests a killer who killed many children. He and Scully realize that Samantha had been abducted but grown up with CSM and Agent Spender when they were young. She was experimented on and ran away. Eventually, a Walk-in took her away and Mulder is reunited with her spirit in a forest.
Mulder and Scully investigate a potential alien abduction case at the site of their first case in Oregon. Meanwhile, CSM (now in a wheelchair) summons Marita and Krycek to him with the intention of starting the Syndicate’s project back up. Krycek and Marita instead tell Skinner, Mulder and Scully about a plan for aliens to take a group of abductees again in Oregon. Scully feels ill so Mulder and Skinner investigate and Mulder is abducted by a UFO along with the other abductees. Krycek and Marita again meet with CSM who is aware their plan is failed and the two toss him out of his wheelchair down a flight of stairs to kill him. Back in D.C., Scully tells Skinner she isn’t sure how, but she is pregnant.
Scully teams up with Agent John Doggett in a taskforce to find Mulder. They instead find Gibson who is being hunted by the Alien Bounty Hunter, who disguises himself as several FBI agents. Ultimately, Scully shoots him in the neck and kills him. Mulder is shown to be held in a UFO with six other Alien Bounty Hunters observing him. While Scully and Doggett are unsuccessful, the two are assigned to the X-Files which Scully hopes could eventually lead to Mulder.
Scully later investigates a case involving abducted women who have reportedly been impregnated with alien babies which makes her question her own mysterious pregnancy. Along the way, Scully and Doggett come to believe the military is trying to cover up these pregnancies and portray them as normal. Doggett gets in touch with an old military friend, Knowle Rohrer, and asks him to look into one of the husbands of the women, who he suspects is a CIA agent. Later, a spaceship dumps a naked woman in the middle of a road and the FBI learn she was abducted at the same time as Mulder. While at a hospital, Jeremiah Smith appears as a doctor and has her transferred. Doggett involves an old FBI partner, Agent Monica Reyes, to find the missing woman. Reyes tracks the woman to a doomsday UFO cult where they arrest the leader but cannot find Smith. Video footage shows Smith shape-shift into Doggett and they all race back. Scully holds Smith at gunpoint but is distracted when Skinner says they found Mulder’s body in the woods outside. They bring his lifeless body back to the compound where Scully asks Smith to heal him but a UFO shows up and Smith and Mulder disappear in a bright light.
Three months after Mulder’s funeral, the body of the first abductee Mulder and Scully investigated turns up but revives on the coroner’s table. Skinner immediately orders Mulder’s body to be exhumed and they find he has weak signs of life. Krycek blackmails Skinner with his nanobot virus, saying he can give a cure to Mulder’s alien virus if Skinner makes sure Scully’s baby is not born. Instead, Skinner begins to unhook Mulder from life support, which ultimately begins to revive him along with Scully’s medical help.
A man tries to jump the White House fence and gets himself killed. He was trying to deliver a disk that reads “Fight the Future.” Meanwhile, Doggett meets the UFO doomsday cult leader who believes marks on the back of someone’s neck can indicate if they are an alien. Mulder and the Lone Gunmen are told by Doggett that his military contact, Rohrer, says the phrase on the disc is a password and they hack into the Census database. Doggett warns Mulder that the password is a trap and they escape just in time to evade military black ops tracking them. Doggett confronts Rohrer over his advice but Rohrer claims he was just showing Doggett what he’s up against. Unseen by Doggett are marks on Rohrer’s neck.
A later case involves the Black Oil showing up on an oil rig in the Gulf of Mexico. It kills everyone except one man who instead gets some radiation burns. Scully thinks his Native American heritage may provide an immunity to the Black Oil. Mulder is ordered not to work on the investigation but does so and is dismissed from the Bureau by Assistant Director Kersh.
Krycek later tells Skinner and the X-Files agents that the aliens have begun eliminating any evidence of their collaboration with humans, killing scientists that worked on the human-alien hybrid, vaccines, and so on. Rohrer tells Doggett that the military created some genetically altered super soldiers but it is a cover story for the fact that several alien Super Soldiers have inserted themselves into the FBI and U.S. government to cover up their history. Krycek betrays the team and Skinner ultimately shoots him in the head. Scully gives birth to an apparently normal baby boy while surrounded by Super Soldiers but they inexplicably leave when Mulder arrives. Mulder and Scully welcome their son, William, and take him to Scully’s apartment.
Mulder has gone into hiding and Scully refuses to tell anyone where he went. Doggett, Reyes and Scully investigate a conspiracy to place Chloramine in the nation’s water supply, mutating them into Super Soldiers, but stop it. Meanwhile, William appears to exhibit supernatural abilities, making his crib’s mobile move on its own. Their investigations are slowed down by Deputy Director Kersh and Assistant Director Follmer.
Later, a stranger offers to take Scully to Mulder but it is a trap. He’s a Super Soldier who fails to kill Scully. Eventually, Scully, Doggett and Reyes find evidence of a UFO cult who came across a craft similar to the one Scully encountered in Africa. The cult kidnaps William but they are killed when William’s crying activates the ship and it destroys everyone except William.
Doggett encounters a disfigured man in the X-Files office, who he thinks could be Mulder. A DNA test shows it could be. He asks for some files and Scully takes him to her house to share them. William is crying but stops when the man picks him up. He tells Scully that William’s abilities are because he is part alien but he has a cure. Scully allows him to administer something that does remove his powers. The man revels that he is actually Jeffrey Spender and he did this out of spite for his father, the CSM. CSM has survived and started a new conspiracy involving the Super Soldier aliens replacing people in the government. And that the aliens needed William’s abilities to move forward with their plan. Now they cannot but they will still search for William. So Scully gives him up for adoption.
Mulder comes out of hiding to look for classified information on an Army base and kills Super Soldier Knowle Rohrer. He is captured and placed on trial. Kersh, Scully, Reyes, Doggett, Spender and Gibson testify on his behalf and help him escape. Mulder and Scully travel to New Mexico to get information from a “wise man” but it turns out to be the CSM who claims the aliens will colonize Earth in 2012. Doggett and Reyes are attacked by Rohrer who is still alive but is then killed by magnetite, the only weakness of Super Soldiers. The four agents run away from black ops helicopters which fire missiles intended to kill Mulder but that instead kill the CSM. Mulder and Scully are together in a motel, and admit they face an uncertain future.
X-Files: I Want to Believe (movie)
Six years later, Scully works as a doctor in a hospital and Mulder lives with her, living off the grid. The FBI contact Scully and tell her about a missing agent case. They want Mulder’s assistance and forgive any past transgressions for his help.
Eight years later, new evidence of alien invasion is found by a right-wing web show. Skinner brings in Mulder and Scully to hear him out. Mulder discovers evidence of the government using alien technology and comes to believe there was never an alien colonization planned, but rather a conspiracy of men to fake abductions, using alien technology. Mulder and Scully are rehired and assigned to the X-Files. Six weeks later, people begin to get sick. Ultimately, it turns out everyone in America has been infected with alien DNA and the CSM has activated it as the Spartan Virus, which turns off immunity to disease. Agent Reyes explains it to Scully. Reyes has been working for the CSM for 12 years. He survived and apparently rebuilt the Syndicate. Reyes has been trying to stop them from the inside, delaying their planned-for-2012 Spartan Virus attack. Scully is able to identify alien DNA in herself and fashion a cure for the virus from it. She races to get to a very sick Mulder but finds that it isn’t enough to cure him. The only thing that could is stem cells from their son, William, but she doesn’t know where he is since giving him up for adoption. Just then, a UFO shines a light on them from above.