The second season of the science fiction television series The X-Files commenced airing on the Fox network in the United States on September 16, 1994, concluded on the same channel on May 19, 1995, after airing all 25 episodes. The series follows Federal Bureau of Investigation special agents Fox Mulder and Dana Scully, portrayed by David Duchovny and Gillian Anderson respectively, who investigate paranormal or supernatural cases, known as X-Files by the FBI.
The second season of The X-Files takes place after the closure of the department following the events of the first season finale. In addition to stand-alone "Monster-of-the-Week" episodes, several episodes also furthered the alien conspiracy mythology that had begun to form. Season two introduced several recurring characters—X, an informant to Mulder; Alex Krycek, Mulder's partner-turned-enemy; and the Alien Bounty Hunter, a shape-shifting assassin.
The storylines were widely affected by the pregnancy of actress Gillian Anderson; it was decided that Scully would be kidnapped and abducted by aliens, explaining her absence and allowing her to appear comatose two episodes later, which ultimately added more intricacies to the mythology. The season earned seven Primetime Emmy Award nominations. The premiere "Little Green Men", debuted with a Nielsen household rating of 10.3 and was viewed by 9.8 million households, marking a noticeable increase in viewership since the previous year. The series rose from number 111 to number 63 for the 1994–95 television year. In addition, the show's second season has generally received positive reviews from television critics.
After the death of Deep Throat and the closure of the X-files, Mulder and Scully are separated and re-assigned. Scully returns to her teaching position at the FBI Academy, Quantico. And Mulder bogged down in mundane phone tap surveillance work begins to lose faith in his search for the truth, after everything he has been witness to in the X-files, he has no hard evidence to prove the existence of extraterrestrials and his sister's abduction. Mulder is called by his contact on Capitol Hill, Senator Matheson who questions Mulder on his knowledge about the Voyager spacecraft sent out in to the cosmos with a message from mankind. Senator Matheson explains that the abandoned Arecibo ionosphere observatory in Puerto Rico had received a signal for outer space, that appears to be information from the Voyager message. With a Blue Beret UFO Retrieval Team already on route to destroy the evidence, Mulder goes AWOL in Puerto Rico to the abandoned SETI Program site, in search of contact with intelligent alien life forms. Scully is questioned about Mulder's whereabouts and manages to trace him via evidence at his apartment and one of his pseudonym's 'George E Hale' on a flight manifest to Puerto Rico. But as Scully finds Mulder so does the Blue Beret UFO Retrieval Team. In their rush to leave most of the evidence is left behind. Back in Washington Mulder finds the evidence he does have is worthless. However he has found the faith to keep looking for the truth.
Mulder is pulled of his mundane phone tap surveillance assignment and sent to investigate the discovery of a decomposing body in the New Jersey sewers, but Mulder dismissing it as another gangland killing. Insulted by the pointless assignment he storms in to Assistant Director Skinner's office and confronts him. Skinner tells Mulder the X-files have been closed and the sooner he accepts that the better. Mulder later confesses to Scully that he is considering leaving the bureau and pursuing his interest in the paranormal on his own. But Scully, handling her reassignment more professionally, insists on doing the autopsy and discovers a parasitic worm in the dead man's body. When a sewage worker is attacked by something in the same sewers, Mulder interviews the victim in hospital, he has a large unidentified bite mark on his back from the attack. Mulder receives a phone call, an unknown male voice tells him he has a friend at the FBI. Mulder assuming Scully has been talking about him leaving, asks her not to start any crusades for him, but Scully denies any knowledge on the phone call. When the sewage worker is later found dead in his apartment, Mulder realises that the worm is merely the lava stage of a larger creature, that the perpetrator in the murders is a mutant flukeworm. Scully's investigation reveals the new species arrived on a ship used to dispose of material from the Chernobyl accident. Scully concludes that nature didn't make it, mankind did.
When the small town of Franklin, Pennsylvania is rocked by a series of 'spree killings' the local Police requests the FBI's help. Agent Mulder is assigned the case and meets Sherrif Spencer at the latest crime scene, where a real estate agent went beserk in a lift, killing people with his bare hands until police arrived at the scene and shot him dead. It matches the pattern of a number of recent incidents involving individuals with no previous history of violence or anti-social behaviour suddenly going on a killing frenzy in a public area until the police use deadly force to stop them. In each case an electronic device was damaged at the scene. When a car mechanic is found murdered in his garage, Mulder notices that he was repairing a damaged electronic clock display in a car. Mulder questions the car's owner Bonnie McRoberts, but she attacked him with a knife and is shot dead by Sheriff Spencer. Scully autopsies Bonnie's body and finds high levels of adrenalin and a substance called LSDM. The Lone Gunman explain that LSDM is an experimental synthetic insecticide that releases pheromones that induce a fear response in cluster flies. It seems that local officials sanctioned the spraying of LSDM on crops, that the local local economy depends on to save them from cluster flies. Mulder believes that LSDM is causing the same fear response in a minority of local people, those who suffer from cronic phobias. But evidence merges that someone may be using the town as a controlled experiment.
Mulder receives an audio tape in his morning paper, which draws his attention to the death of Dr Grissom, a prominent doctor specialising in sleep disorders. The tape is a recording of the 911 call, from the tape it is clear that Dr Grissom believed his apartment was on fire. But the newspaper article does not mention a fire. Mulder manages to get himself assigned to the case only to find that another agent, Alex Krycek has been assigned the case. Mulder reluctantly has to partner him for the period of the investigation. Scully performs the autopsy on Grissom and discovers that his internal injuries are consistent with being burned to death in a fire, as if his body had thought it was being burned. When a second man, Henry Willig, found dead in his apartment is autopsied Scully discovers that he has internal wounds that indicate he was shot to death. Mulder is contacted by a mysterious man X, who sent him the audio tape. X is a colleague of Mulder's former contact Deep Throat, who tells him that he is in a position to help Mulder, but on his terms. X tells Mulder that Willig and Grissom were both involved in a sleep eradicate experiment on a group of elite Vietnam soliders known as J7. Evidence emerges that one of the two surviving members of the squad, Augustus Cole is atoning for their sins during the war. Mulder believes that in his years without sleep Cole has developed the ability to project his thoughts on to other people and is using this power to kill.
Mulder finds himself partnered with agent Krycek once more, when their assistance is requested in a hostage situation in Richmond, Virginia. An escapee for a psychiatric hospital is holding his doctor and three employees hostage in a travel agents' office. The man, Duane Barry an ex-FBI agent claims to be a multiple abductee who is taking his doctor to the next abduction site to prove his story. Only he can not remember where the site is. The agent in charge wants Mulder to head up the negotiation because of his expertise with UFO abductions. But as the negotiations begin the office suffers a power cut and Duane Barry fearing it is an abduction attempt accidentally wounds one of the hostages. Mulder goes in disguised as a medic to try to talk to Duane Barry. Despite warnings from the hostage team, it is not long before Mulder is buying into Duane Barry's fantasies. And Duane Barry has never found anyone who believes his claims and begins to open up to Mulder. Meanwhile Scully carrying out some background checks is concerned for Mulder's safety when she discovers that Duane Barry was shot in the head in 1982 and suffered an injury that left him a pathological liar. Mulder safely negotiates the release of the other hostages apart from the doctor who Duane Barry wants to take to the abduction site to be taken instead of him. However Duane Barry is shot by a police marksman and rushed to hospital, but he later escapes and kidnaps Scully.
There is a message on Mulder's answer phone from Scully, the recording includes the sound of Scully being attacked. Mulder rushes to Scully's apartment only to find the police are already there. There are signs of a struggle, Mulder realises that Duane Barry has kidnapped her. Margaret Scully, Scully's mother arrives at the scene and she tells Mulder that she had a dream that her daughter had been taken. But Mulder re-assures her that he will find Scully. Assistant Director Skinner removes Mulder from the FBI investigation telling him he is too close to the case. However when a patrolman is killed by Duane Barry, video footage from his patrol car shows that Scully is still alive. From the route Duane Barry is taking and his description of the abduction site in the travel agents office Mulder concludes that he is heading for Skyland Mountain in Virginia. Mulder and Krycek travel to Skyland Mountain, they discover that Duane Barry has already driven up the mountain road. Mulder gets the operator to turn on the cable cars in an attempt to head Duane Barry off at the summit. However Krycek kills the operator and reverses the cable car, Mulder manages to reach the summit by leaping to another cable car, but he is too late to save Scully. Mulder arrests Duane Barry who claims that the aliens took Scully instead of him, before Mulder can question him further he dies in the presence of Krycek. Mulder attempts to bring charges against Krycek, but the FBI can find no trace of him.
With Scully still missing and no one to trust, Mulder is forced to immerse himself in his work on the recently reopened X-files. Mulder opens an X-files case (No. 73317) on Scully's abduction, before being contacted by the LAPD, who are investigating a murder where the victim was drained of his blood. Mulder recognises it as the work of a trio of serial killers called the 'Unholy Trinity', who he has been following for over a year. They previously struck six times in Oregon and Tennessee. They have a fetish for drinking the blood of their victims. The LAPD busy with a raging forest fire are more than happy to hand the case over to Mulder. Mulder rings around the local blood banks to see if any have recently taken on new employees. A ploy which pays off as he catches one of the killers John drinking blood in the basement of the Hollywood Blood Bank. John who calls himself 'The Son' claims he ingests blood because he is a vampire who can not die, but Mulder believes John is delusional. John is placed in a cell for the night but when the sun rises in the morning he is burnt to death, much to Mulder's surprise. During the autopsy on John's body, a stamp is discovered on his hand that leads Mulder to the Club Tepes. At the club Mulder meets a vampire fetishist called Kristen. She knows John, they used to be in to blood sports together but then it all turned unnatural. Now he is dead she fears for her safety. Mulder has trouble determining whether Kristen is a criminal or a victim.
Scully appears in the Georgetown Medical Centre, Washington without any explanation for her condition. She is unconscious and on life support in a critical condition. Mulder feels helpless as her mother Margaret and sister Melissa make decisions about her condition, as a doctor Scully had specific criteria for the termination of life support, her living will which Mulder witnessed states she would not want to live in her current condition. Frohike from The Lone Gunman visits the hospital and steals Scully's medical chart. The Lone Gunman study the chart and inform Mulder that Scully's blood is contaminated with redundant DNA the result of genetic experimentation, the outlook is not good. Mulder sees a man taking a vial of Scully's blood from the hospital and chases him. In the basement car park he fights with the man before X emerges from the shadows and kills the man. X warns Mulder to desist from his investigation of the people responsible for Scully's condition. Scully's family honour her wishes and terminate the life support keeping her alive. Mulder visits Assistant Director Skinner and demands the mysterious Cigarette Smoking Man's address, who he believes to be responsible. Mulder visits the Cigarette Smoking Man and pulls a gun on him. But Mulder realises killing him will not help Scully and will only make Mulder more like the shadowy men who work against him. Later he receives a phone call informing him that Scully has regained consciousness.
When contact is lost with a volcanic research team working on Mount Avalon, Mulder and Scully are approached by Adam Pierce, a technician at the Californian Institute of Technology's Volcanic Observatory. Pierce is able to remotely activate the cameras on the research team's survey robot, Firewalker. The picture shows the dead body of one of the members of the team and the shadow of something moving around in a cavern with temperatures in excess of 300 degrees. Pierce asks Mulder and Scully to join him in an investigation. Mulder is concerned about Scully condition following her recent abduction and return but Scully tells him she is back working on the X-files. When they arrive at Mount Avalon, they find three members of the research team, Jason Ludwig, Jesse O'Neill and Peter Tanaka. They describe how the team leader Daniel Trepkos went berserk, smashed the radio and destroyed the base. Shortly after Pierce is strangled by Trepkos. Meanwhile Mulder uncovers Trepkos' notes which seem to indicate the discovery of a silicon based life form living in the Volcano. And that Firewalker accidentally brought back this fungal life form which infected the members of the research team. Trepkos is killing the infected members to ensure the infection does not spread. Scully's medical expertise is invaluable once more, her research indicates that infection only occurs if a person is exposed at the moment that the fungal spores are released, so Trepkos lets them leave.
Mulder and Scully are called in to investigate by a local sheriff after a number of Wisconsin teenagers are found walking in the woods in their underwear, drugged and with the phrase 'He is one' or 'She is one' written on their bodies. Sheriff Mazeroski believes a local religious cult called the Church of the Red Museum is responsible. They came to the area three years before and bought a ranch, being vegitarian they turned the cattle in to pets, which caused a lot of resentment with local cattle ranchers. But after going to see them Mulder informs Scully they are 'walkins', who believe in soul transference, that enlightened souls take over other peoples bodies. Mulder doubts their complicity, however he notices their presence causes a lot of tension in the local community. An old man shows Mulder and Scully cattle being injected with a genetically modified growth hormone, which he claims has made the local people very aggressive. The case takes a dramatic turn when the local doctor is killed in a light aircraft accident. His briefcase contains thousands of dollars, details of local families and a phial of liquid. Later identified as similar to the substance found in The Erlenmeyer Flask. It would appear that Dr Larson was injected local children with the contents of the phial. And that the attacks on the teenagers was an attempt by a local paedophile to draw attention to these experiments. But they have to move fast as the evidence begins to disappear and witnesses start to die.
Mulder and Scully investigate when the rape and battery of a nurse takes place in a Massachusetts convalescent home. The nurse claims that she was attacked by one of the residents but also claims they were invisible. Mulder and Scully soon discover that it may not be one of the residents after all...
When Aubrey police detective B.J. Morrow uncovers the body of an FBI agent missing for nearly 50 years in a field but can not explain how Mulder is suspicious. Dental records confirm the body is that of agent Sam Chaney, both he and his partner Tim Ledbetter used psychology to solve what were called 'stranger killings' in the 1930's. But they disappeared in 1942 while investigating a series of 'slash killings' in Missouri. Mulder and Scully interview Morrow, she claims that when her car stalled, she noticed a dog digging in the field and then discovered the body. Mulder and Scully meet Morrow's superior Lieutenant Tillman, Scully realises that their relationship is more than professional. When Scully questions Morrow, she admits that she is having an affair with Tillman even though he is married. She also tells Scully that she is pregnant and has been having dreams about murders since she has been pregnant. Mulder believes that Chaney and Ledbetter fell victim to the 'slash killer' that they were tracking in 1942. A killer who attacked women and carved the word, 'sister' in to their chests. When he discovers the marks on Chaney's ribs spell out the word, 'brother' he is convinced they were killed by the same man. When Tillman sees the crime scene photographs that Mulder has on the 1942 'slash killings', he is shocked. As he is currently investigating a series of attacks on local women matching the same MO. Mulder soon realises that Morrow's dreams hold the key to the case.
When FBI agent Moe Bocks of the Minnesota Bureau investigates the case of a female corpse dug up and mutilated, he is quick to think it is the work of extraterrestrial and calls in agent Mulder and Scully for their expertise with UFO's. However Mulder who has seen this before recognises it as the work of an escalating fetishist. Someone who collects dead things, hair and fingernails, no one quite knows why they do it. Scully who has never seen a case like it before although she has read about them, is badly shaken by what she sees. Mulder warns agent Bocks that the escalating fetishist may progress from mutilating the dead to opportunistic homicide, killing people and then mutilating them. A theory given credence when a prostitute is found murdered and mutilated. After examining the body and how it was defiled Mulder tells Bocks that the killer has a deep hatred of women and will continue to kill until he is stopped. As word of the attacks spreads the local populous become uneasy, when a prostitute is hit by a john she pulls a knife and cuts him. Mulder and Scully joins Bocks as they question the man, who it turns out is innocent. But unknown to them the fetishist, Donnie Pfaster is in the next cell. Scully struggling with her reaction to the case goes back to Washington with the prostitute's body, a move which pays off when she finds a latent fingerprint. But on her return she is intercepted and kidnapped by Pfaster and Mulder has to pull out all the stops to find her before it is too late.
After a group of teenagers fake an occult ritual at a woodland alter, inadvertently causing the death of one of their group, something evil is unleashed in the local community. Mulder and Scully are called in by the local police who fear the involvement of witchcraft. They travel to New Hampshire to investigate, combing the scene where teenager Jerry Stevens' body was discovered, they are caught in a down pour of toads! Later in Crowley High School Mulder notices the water running backwards down the drains, indicating that something powerful is affecting the area. When local teenager Shannon Ausbury, one of the group present at the occult ritual where Jerry died, comes forward with claims of repressed memories of occult rituals, sexual molestation, that she was made pregnant and then the baby sacrificed. Mulder and Scully are stunned and question Jim and Barbara Ausbury about their daughters claims. The Ausburys are incredulous and dispute their daughter story, Shannon has never been pregnant. Before they can question Shannon further she slits her wrists during a lesson with Mrs Paddock, a substitute teacher that no one can remember hiring. Jim Ausbury meets with a group of parents in secret, they discuss how they have let their religion slip, how they feel the presence of something evil in town. They attempt to re-affirm their beliefs before it is too late. But it would appear it will take much more to appease the evil presence among them.
Mulder and Scully respond to a request by Robin McAlpin to investigate the events surrounding the death of her marine husband Private Jack McAlpin in North Carolina. He is the second marine stationed at the Folkstone government processing camp for Hatian refugees to die in mysterious circumstances. The Marine Corp officially classified the deaths as suicides, but another marine stationed at the camp, Harry Durham attributes the deaths to a voodoo curse. Mulder and Scully travel to the camp and interview the base commander Colonel Wharton. He tells them that tension has been high in the camp since a young Haitian boy was killed during a riot. He blames the whole situation on a Haitian revolutionary, Pierre Bauvais who is being held in a camp cell. Scully is given permission to carry out an autopsy but McAlpin's body is missing. However as she and Mulder drive away from the camp, she narrowly avoids running down McAlpin walking in the middle of the road. Tests on McAlpin reveal trace amounts of the poison tetrodotoxin in his blood stream, leading Mulder to conclude that someone injected McAlpin so that he would appear to be dead. When Durham makes a claim that Commander Wharton has sanctioned the beating of the refugees in retaliation for the men he lost during the invasion of Haiti, the situation is further muddled. In the charged world of voodoo curses and zombie soldiers Mulder and Scully search for the truth behind the deaths.
Anonymous email postings draw the attention of Mulder and Scully to the deaths of two identical doctors, killed in arson attacks on abortion clinics up and down the north eastern states. With one outstanding feature, no bodies were recovered from the ashes. Mulder and Scully discover that someone is running newspaper adverts with a picture of the doctor, trying to find other look alikes across the country. When they manage to track one down, a doctor living in Syracuse, they get a local FBI Agent to protect the doctor until they can get there. But when they arrive agent Weiss tells them that the doctor is gone. On his return to Washington Mulder is called to Assistant Director Skinner's office, agent Weiss has been found dead in Syracuse and Mulder is held accountable. Taken off the case by Assistant Director Skinner, Mulder and Scully are approached by CIA agent Ambrose Chapel who makes claims that the doctors are Russian clones left over from the Cold War, planted in the US to carry out sabotage in the event of war. That the doctors are being killed off to cover the existence of the Russian's cloning program. Mulder is once again contacted by Assistant Director Skinner, who tells him he has a family emergency. When Mulder arrives home, his father Bill meets him on the porch. As they talk Mulder notices his mother, Teena talking with a young woman, when he asks his father who she is, Bill Mulder tells him that his long lost sister Samantha has been returned. Part One
Samantha confides in her brother, telling Mulder she was returned to earth some time ago and has been living with 'visitors' to the planet. The doctors who all look alike are really alien clones living on earth, just like her adopted father. But the colony is under threat from an alien bounty hunter sent to kill them. Meanwhile Scully is taken hostage by the mysterious alien bounty hunter who has the ability to morph himself to look like other people. He demands to know where Mulder is but Scully refuses to co-operate. The alien bounty hunter holds Scully ransom in exchange for Samantha. Mulder sets a trap for him with the help of Assistant Director Skinner, but it goes awry and the alien bounty hunter and Samantha tumble off a bridge in to the water below. Mulder is devastated at loosing his sister again so suddenly and has to break the news to his parents. Bill Mulder gives Mulder a letter that Samantha left for him should anything happen to her. It contains a key and the address of an abortion clinic. Mulder goes there and encounters more 'Samanthas', it turns out one of them pretended to be his sister Samantha in an attempt to get him to protect them. But they are too late as the alien bounty hunter finds them and kills the last of the clones. Mulder risks his life and tracks the alien bounty hunter in a effort to find out about his sister but ends up being exposed to a toxic alien poison and is left for dead high up in the arctic. Scully tries desperately to find Mulder before it is too late. Part Two
Mulder and Scully are called in to investigate after the death of a federal employee and the destruction of personal property is linked to an escaped elephant, despite the fact that no witnesses saw the creature. Mulder and Scully travel to Idaho and meet Ed Meecham, the elephant trainer at the Fairfield Zoo who shows them that the elephant's cage is still locked. He suggests they talk to Willa Ambrose, a naturalist hired by the zoo to develop more suitable habitat for the animals. She explains that she was hired to improve conditions at the zoo after pressure from an animal activist group called the Wild Again Organization. She also tells them to talk to Kyle Lang, a member of the WAO. Their meeting leads Scully to believe that the WAO is to blame, a theory given credence when a member of the group is mauled to death by an escaped tiger while attempting to break in to the zoo. However Mulder confers with Frohike and Byers of The Lone Gunman via a satellite linkup. They inform him that the Fairfield Zoo is renowned for never having had a successful live birth in captivity. Which leads Mulder to the conclusion that extraterrestrial are impregnating the zoo animals and harvesting the embryos as part of a conservation plan. When Mulder expresses his theory to Willa Ambrose she is incredulous until Scully's autopsy on the elephant reveals that it had been pregnant in the past. It seems the only place to find the answers is in the cage of a hand signing gorilla.
When the U.S.S. Ardent disappears off the Norwegian coast just below the 65th parallel, an area Mulder refers to as the second Bermuda Triangle, where nine other vessels have disappeared since 1949. Mulder arranges for Scully with her medical background to gain access to the sole survivor Lieutenant Richard Harper at the Bethsheda Naval Hospital in Maryland. Scully is surprised to find that the 28 year old Harper is a wrinkly grey haired old man. Mulder believes it has something to do with the Philadelphia Experiment during World War II, a government project to render ships invisible to radar, which Mulder claims used technology recovered from the infamous Roswell Incident. Mulder and Scully travel to Norway to investigate, but find it difficult to get anyone to take them out to the area. Only Henry Trondheim captain of the local trawler Zeal is willing to take them. They find the U.S.S. Ardent dead in the water, a rust covered old ship despite the fact that is was only commissioned in 1991. As they explore the ship the trawler Zeal is hijacked and sails away leaving them stranded on board. They encounter a local pirate whaler Olafssen, who seems unaffected by premature ageing. They realise his apparent immunity holds the key to the case. As Mulder and Scully begin to age rapidly Scully theorises that if the U.S.S. Ardent was drifting towards a meteorite on the ocean floor, the resulting electromagnetic energy could be exciting free-radicals, the elements believed to cause ageing.
When Jerald Glazebrook aka 'Alligator Man' is attacked and killed in Gibsontown, Florida a retirement community for freaks and side show performers. It matches a pattern of forty-eight similar attacks spanning twenty-eight years all across the US. Someone working in circuses travelling from place to place across the US would be a primary suspect. Mulder and Scully investigate the recent attack in an attempt to catch the killer. They meet with Sheriff Hamilton who fills them in on the case. Mulder is intrigued by a drawing by local artist Hepcat Helm of the Fiji Mermaid, an exhibit P.T. Barnum billed as a 'genuine fake' as it was supposedly a fish's tail sown on to the body of a monkey. When Hepcat Helm is later killed in his studio and the only access is via a very small window, Mulder theorises that the Fiji Mermaid is not only real but responsible for the murders. As they later discover that Sheriff Hamilton himself used to be Jim-Jim, the dog-faced boy and encounter other town residence like Dr Blockhead who performs human feats of endurance and The Conundrum, a tattooed jigsaw man who eats live animals. Scully finds it difficult to find a normal suspect, in a place where nothing is normal. Her suspicions fall on trailer park porter Lanny's congealed twin Leonard, as Scully theorises that Leonard is capable of extracting himself from his brother's body. Lanny later confirms this but claims that Leonard does not mean to hurt people, he is merely searching for another brother.
When two year old Teddy Holvey chases a balloon in to the path of an oncoming miniature train at the Lincoln amusement park, Virginia. A picture taken moments before the tragic accident shows the balloon moving against the wind, Mulder has the picture graphically enhanced, which reveals the shadowy figure of a child pulling the balloon along. Leading Mulder to believe that poltergeist might be involved. Mulder and Scully go to Arlington to interview the boy's family. They speak with Steve and Maggie Holvey about their son's accident. Maggie is originally from Romania and her mother has been living with them since Teddy was born. They have another son, eight year old Charlie, his Grandmother is both protective and fearful of him, leading Scully to believe that it is a case of Munchausen's-by-proxy. A rare form of child abuse when a parent or guardian brings harm to the child to get attention. When Steve Holvey is later killed in a bizarre accident, ash from the scene is identified as a substance called Vibuti, holy ash produced during the presence of spiritual beings. The Grandmother later dies while performing a protective ritual on Charlie and when a social worker questions Charlie about the incident, he claims his still born twin brother Michael killed her. Which comes as a shock to Maggie Holvey, who claims she never told Charlie about his dead twin brother. It appears that the families only hope is a strange group of Romanian elderly chanters called The Calusari.
When Assistant Director Skinner assigns agents Mulder and Scully to assist the Federal Marshals office in a man hunt for two escaped prisoners, they are confused about the reasons for the involvement of the FBI. On their arrival at Cumberland State Correctional Facility, Scully discovers a break out of a highly contagious and deadly disease in the prison. She questions Dr Osbourne, who claims to be from the Centre for Disease Control. A flu-like condition has claimed the lives of ten inmates and the two escaped prisoners may also be infected. As Scully enters the prison to see if she can help. Mulder joins the man hunt to track down the two fugitives before they contaminate the public. Further investigation by Scully reveals that patient zero, Bobby Terence received a package from Pinck Pharmaceutical just before the contagion broke out. Dr Osbourne, who works for Pinck Pharmaceutical not the CDC, is accidentally infected and near death explains to Scully that the company funds exploration of rain forests for potential drug application. One of their entomologists discovered an insect Faciophagia Emasculata, which carries a parasite that attacks the human immune system. Now the company and the government are attempting to cover up the fact that the prisoners were used as guinea pigs. When Mulder and Scully discover the involvement of the Cigarette Smoking Man, they suspect the whole incident is an attempt to eliminate them and debunk the X-files.
Detective Kelly Ryan, one of Scully's ex-pupil at the academy asks for her assistance on her first ever case. Three people have vanished without a trace, the latest victim, Patrick Newirth disappeared from his locked hotel room leaving only a black smear on the floor near the door. Mulder toys with the idea of spontaneous human combustion. However when they discover that all three victims passed through the Richmond train station, Mulder and Scully review the station's security footage, a move rewarded when Mulder notices a man sitting at one spot in the station acting strangely. On the video they can make out the badge he is wearing which leads them to a company called Polarity Magnetics. They show a photo of the man in the station to Dr Davey, who identifies him as his colleague Dr Ray Banton, who was researching dark matter. But Dr Banton has not been seen since he accidentally exposed himself to a massive amount of energy that burnt his shadow in to the wall. Mulder and Scully stake out the station and when Dr Banton appears, they attempt to arrest him. Dr Banton warns them not to touch his shadow, Mulder realises that his shadow is deadly and arranges for him to be taken in to custody safely. However Detective Ryan and her department block Mulder and Scully from further access to Dr Banton. Frustrated Mulder contacts X about the case, but X tells him he can not help. Later X kidnaps Dr Banton and delivers him to a government laboratory to be tested on.
Mulder and Scully travel to Dudley, Arkansas to investigate the disappearance of Federal Poultry Inspector, George Kearns. Aided by Sheriff Arens, they examine a field where witnesses reported seeing fox-fire on the night Kearns went missing. Mulder suggests some sort of ceremony took place in the field, but the Sheriff dismisses it as an illegal trash burn, nothing more. The interview Kearn's wife who tells they that he probably ran off with a younger woman. The Agents visit the local Chaco Chicken processing plant, which Kearns was about to recommend be closed down due to health violations. While they are there one of the workers, Paula Gray goes crazy and takes her supervisor hostage but Sheriff Arens shoots her dead. Mulder and Scully visit the plant's owner Walter Chaco, Paula was his granddaughter, they request permission to do an autopsy on her and he agrees. Scully discovers signs that Paula was suffering from Crutzfelt-Jacob's disease, the rare but non contagious disease that Kearns had. She also discovers that Paula is forty-seven old, however she looks to be in her early twenties. When a statistically impossible number of the local population also contract Crutzfelt-Jacob's disease, Mulder begins to get suspicious. He orders the dredging of a local river used as run out from the plant, which leads to the discovery of a number of mutilated skeletons. Mulder and Scully begin to suspect that chicken is not the staple diet of the local towns folk.
When the newest member of the The Lone Gunman, the Thinker, hacks into the Defense Department's secret files on extraterrestrial life and he gives the Dat tape to Mulder to expose the truth. Mulder who has been suffering from sleeping problems is at first disappointed to find that the information is encrypted, but Scully recognises it as Navajo code used during World War II. Mulder is called to Assistant Director Skinner's office and questioned about the Dat tape, but Mulder punches Skinner. Mulder can not explain why he hit Skinner and Scully is alarmed at his behaviour. The Cigarette Smoking Man is also working to recover the Dat tape and visits Bill Mulder, they used to work together at the State Department and information on the tape implicates Bill Mulder. He contacts Mulder to come and see him, ready to tell his son the truth about his work. However Krycek kills him before he can tell Mulder anything. Mulder finds Krycek sneaking around his apartment building and they fight. Scully has to shoot Mulder in the shoulder to stop him from killing Krycek. Mulder wakes up in New Mexico and Scully explains that the water in his building was contaminated with LSD, which caused his psychosis. She introduces Navajo code talker Albert Hosteen who is decoding the files. Mulder is taken to a boxcar buried in the desert and discovers alien bodies inside. However the Cigarette Smoking Man's men arrive and destroy the boxcar with Mulder in it. Part One