Season 2

S2E1 · Little Green Men

In the episode's prologue, Fox Mulder narrates a history of NASA 's Voyager program and the now-defunct High Resolution Microwave Survey, which sought to contact extraterrestrial life in outer space. At the Survey's abandoned observatory in Arecibo, Puerto Rico, the equipment inside suddenly activates, indicating a response from an alien intelligence.

Since the closure of the X-Files, the FBI has reassigned Mulder to a low-level wiretap while his former partner, Dana Scully, has returned to teaching at the FBI Academy. The two have a discreet meeting at the parking lot of the Watergate Hotel, where Mulder admits that he has been doubting his belief in the paranormal since Deep Throat 's assassination. Mulder flashes back to the night when his sister, Samantha, was abducted.

Mulder is summoned to a meeting with Richard Matheson, a U.S. senator who is a patron for his work. Matheson directs Mulder to Arecibo, assuring the agent that he will try to hold off a Blue Beret UFO retrieval team said to be headed there in twenty-four hours. Arriving at the Survey station, Mulder discovers a frightened Puerto Rican man, Jorge, who cannot speak English but draws a picture of an alien he claims to have seen. Meanwhile, Scully, unaware of Mulder's whereabouts, goes to his apartment looking for him. Reviewing a list of flights from Washington, Scully recognizes one of Mulder's personal heroes' names and tracks him down to Puerto Rico.

Mulder discovers a signal, possibly originating from an extraterrestrial intelligence. During a storm, Jorge panics and runs outside; Mulder finds him dead of fright. When Scully goes to an airport to fly to Puerto Rico, she realizes she's being tracked by a couple but manages to lose them. Meanwhile, as Mulder examines Jorge's corpse, the room shakes. The door opens and the shadowy figure of an alien appears; Mulder tries to shoot it, but his gun malfunctions and he passes out. Scully wakes Mulder up the next morning, finding him excited about the readouts and tapes of the signals—the proof of aliens he has sought for so long. However, the Blue Beret team arrives, forcing them to flee with only a tape reel.

Upon his return to Washington, Mulder is admonished by Assistant Director Walter Skinner and the Smoking Man for his actions. Mulder claims he still has enough evidence with the days missed to prosecute the subject of his assigned wiretap, and that his own phone calls were being monitored. Skinner then demands that the Smoking Man leave the room, and decides to not discipline Mulder. Investigating the tape reel, Mulder finds it blank due to a power surge during the storm, but vows to continue his work regardless.

S2E2 · The Host

On a Russian freighter off the coast of New Jersey, a crewman trying to fix the ship's toilets is pulled into the septic system. His water-logged body appears in the sewers of Newark days later. Fox Mulder is assigned the case and is shown the still-unidentified body. Mulder initially assumes the case is simply a gang-related murder, and angrily confronts Assistant Director Walter Skinner, feeling he has been given this "wild goose chase" as a form of punishment. That night, Mulder talks to Dana Scully, telling her that he is thinking of leaving the FBI. Scully performs the autopsy on the crewman's body, finding a Russian language tattoo on his arm and a flukeworm inside his liver.

In a Newark sewer, a city sanitation worker named Craig is rescued when an unseen creature pulls him underwater. Believing he was attacked by a python, he visits a doctor with Mulder observing. An examination of his back reveals an abnormal four-pointed wound. Shortly afterwards, Mulder receives a call from a mysterious man, telling him he has a friend at the FBI. Scully shows Mulder the flukeworm, whose mouth, though much smaller, matches the wound on Craig's back. That night, Craig dies in his shower after coughing up a flukeworm. Mulder visits a sewage processing plant and, along with a foreman named Ray, finds a large humanoid mutant with a fluke-like mouth.

At the FBI Academy, someone slips a newspaper article under Scully's door enabling her to identify the original body. Mulder and Scully meet at the processing plant and observe the "Flukeman". Skinner wants to prosecute the creature and subject it to a psychiatric evaluation, which Mulder thinks would be difficult. Skinner tells Mulder of Craig's death and admits that this should have been an X-file. Mulder insists that Craig's death could have been prevented if the X-files had remained open, but Skinner implies that the decision came from higher up the chain of command.

That night, as the Flukeman is being transported by van, it escapes its restraints and kills the driver. It hides in a portable toilet, is soon suctioned into a septic truck and is brought back to the sewage processing plant. Meanwhile, Mulder receives another call from the mysterious man, telling him that the X-files must be reopened. Scully tells Mulder that the flukeworm she discovered is a larva, revealing that the Flukeman is capable of asexual reproduction. Meanwhile at the plant, the Flukeman is spotted in a storm drain overflow pipe, with Mulder realizing it is using the drain to make an escape back to the ocean. Mulder and Ray then investigate the overflow pipe, but Ray is pulled underwater by the Flukeman. Mulder rescues him, bisecting the Flukeman at the waist with a sewer grate.

Scully concludes her investigation, hypothesising that the creature was brought to the U.S. by a Russian freighter that was hauling salvage material from the Chernobyl disaster, and that the creature was created in a "soup" of radioactive sewage. Elsewhere, in the drains beneath Newark, the Flukeman's eyes remain open.

In the 2013 comic continuation of The X-Files called Season 10, a two-issue story, "Hosts", continues the story almost twenty years later after the events of this episode. According to the comics, the Flukeman escaped to Martha's Vineyard and began to multiply, abducting multiple beach-goers. The Flukeman and its offspring were nearly all killed, however, by a man revealed to be one of the Chernobyl liquidators. In addition, the story expanded upon the Flukeman's backstory, revealing that he was a liquidator named Gregory, who, after being locked in a sewage tanker truck at Chernobyl, gestated the mutated flukeworm that grew into the original Flukeman after he was exposed to irradiated cooling water from the still-burning nuclear reactor and to flatworms in the sewage tank.

S2E3 · Blood

In Franklin, Pennsylvania, postal worker Edward Funsch (William Sanderson) is informed that he will be laid off at the end of the week. Afterwards, Funsch sees the words "Kill 'Em All" on his machine's digital display. At Franklin's civic center, a middle-aged man in a crowded elevator sees "No Air" displayed on the elevator's LED display, and is the only one who can see the message. Sweating and obviously claustrophobic, he again glances at the LED display. This time it flashes the words "Can't Breathe" and then "Kill 'Em All."

Agent Fox Mulder arrives at the civic center in the aftermath of what looks like a massacre. Sheriff Spencer (John Cygan) explains that the suspect murdered four people from the elevator with his bare hands; his rampage ended when he was shot by a security guard. Spencer notes that seven other individuals have murdered twenty-two people in Franklin in the past six months. Mulder discovers that the LED display in the elevator has been damaged, and that the dead suspect has a green residue on his fingertips. Meanwhile, Funsch tries to make a withdrawal from an ATM, but is greeted with the words "Security Guard", "Take His Gun" and "Kill 'Em All" on the screen. He frustratedly beats the screen before running away, escaping from a confused security guard.

At the FBI Academy, Dana Scully reads Mulder's initial report. The only connection between the murders that he can see is that the suspects all destroyed an electronic device during the killings. Meanwhile, Bonnie McRoberts, another Franklin resident, drops by a repair shop to pick up her car, where a message on an engine diagnostic display warns her that the mechanic is going to rape her. She impulsively kills him with an oil can spout. When Mulder and Spencer question McRoberts the next morning, her kitchen microwave instructs her to kill them. When she grabs a knife and attacks Mulder, she is shot and killed by Spencer.

Scully performs an autopsy on McRoberts' body and discovers signs of phobia including high levels of adrenaline and the same substance found on the elevator killer. She hypothesizes that the substance, when combined with other neurochemicals, produces an LSD -like reaction. As Mulder and Scully build a case, Funsch becomes more psychotic, continuing to see violent messages on electronic displays. Blood is associated in some way with each incident; a volunteer asks Ed to donate blood at a department store and seconds later he sees several violent images flash across a sales display of TV sets, followed by a message to get a gun from the sporting goods department.

Late at night, while investigating an orchard, Mulder is sprayed by a crop-dusting helicopter and ends up in the hospital. There, he sees the message "Do It Now" on television and realizes that when people are exposed to the pesticide, which contains a chemical designed to provoke fear in insects, these subliminal messages are relayed to them on purpose and their phobias are exacerbated enough to cause them to kill. Mulder believes the town is being used as a testing ground by a third party, implying that the government is complicit. Eventually, after being confronted, a city councilman agrees to stop the spraying and test the community under the guise of a cholesterol study.

Mulder and Scully, reading that Funsch has not been tested yet, arrive at his house to find it strewn with smashed electronic devices. Mulder deduces that blood is Ed's phobia and that he has seen the subliminal messages, and an empty rifle case signals that Funsch is going to act on his paranoia. Funsch positions himself at the top of a clock tower overlooking a blood drive and begins shooting randomly. Mulder climbs up to Funsch and overpowers him; Funsch is taken away on a stretcher. Mulder makes a call to Scully to tell her the investigation has been resolved, but sees the message "ALL DONE" followed by "BYE-BYE" suddenly appear on his cell phone display. Scully calls out to Mulder but he is speechless.

S2E4 · Sleepless

In New York City, Dr. Saul Grissom finds a fire outside his apartment. Firefighters arrive and evacuate the building. One man who is being evacuated has a distinctive horizontal mark on the back of his neck; as he is being evacuated, he looks up at Grissom's apartment and smiles knowingly. The firefighters find no fire or any related damage, but discover Grissom's lifeless body in his apartment.

Fox Mulder anonymously receives a tape cassette of Grissom's 9-1-1 call. He tries to take the case, only to learn that another FBI agent, Alex Krycek, has opened it first. Deciding to leave Krycek out of the loop, Mulder calls Dana Scully (Gillian Anderson) and asks her to conduct Grissom's autopsy. He then heads to Grissom's clinic in Stamford, Connecticut, where he is confronted by an angered Krycek. The two travel back to Quantico to see Scully, who says that Grissom's body showed no signs of a fire, but yet seems to have biologically believed it was burning.

Meanwhile, in a Brooklyn apartment, Vietnam veteran Henry Willig is approached by Grissom's killer, a fellow ex- Marine named Augustus Cole. Suddenly, a group of wounded Vietnamese seemingly appear and gun Willig down. Examining Willig's corpse, Mulder and Krycek find a scar on his neck and realize he was in a Marine reconnaissance unit stationed in Vietnam in 1970; he was one of only two survivors, the other being Cole. They head to the VHA hospital in New Jersey where they discover that Cole was discharged, despite the fact that his doctor does not remember doing so.

Mulder meets a mysterious informant named " X ", who gives him information on a secret military project that Grissom performed where he eradicated the need for sleep through lobotomy. X provides him with the name of Salvatore Matola, a squad member who was mistakenly reported as killed in action.

A man matching Cole's description robs a drug store. Mulder and Krycek arrive, but not before two gunshots are heard from the room where Cole is believed to be. It appears that the two officers in the room with him shot each other; Cole escapes. Mulder believes that Cole's years of sleeplessness have provided him with illusionary abilities. Mulder and Krycek meet with Matola soon afterwards, who says that he has not slept in twenty-four years due to the experiment. He reveals that another researcher with the squad, Dr. Girardi, was the one who actually performed the lobotomies.

Mulder and Krycek head to a subway station, where Dr. Girardi is expected to arrive for Grissom's funeral. Mulder sees Cole there, and Cole seems to shoot Girardi, but this is shown to be in Mulder's head. In reality, Cole has captured Girardi and holds him hostage, about to show him a similar fate as his other victims. By searching surveillance footage, the agents track his location and find Girardi wounded. Mulder finds Cole, who is ready to kill himself. Krycek, believing Cole is holding a gun instead of the Bible he is actually holding, shoots him, and Cole dies of his wounds. Mulder and Scully find both of their files on the case missing.

Krycek reports to the Smoking Man and others, telling them that the dissolution of the X-Files and the separation of Mulder and Scully has only made their determination stronger. He also notes that Scully is a bigger problem than they anticipated.

S2E5 · Duane Barry

In 1985, at his home in Pulaski, Virginia, Duane Barry (Steve Railsback) is abducted by aliens. Nine years later, Barry has become a violent patient in a mental institution, refusing to take his medication and insisting that the aliens are coming back for him. He attacks a security guard and steals his gun, taking head psychiatrist Dr. Hakkie hostage before escaping. Barry seeks to return to his original abduction site with Dr. Hakkie, in the hopes that the aliens will take the doctor instead when they return. But since he can't remember where the abduction site is located, Barry heads to a travel agency in Richmond and holds the three clerks hostage along with Dr. Hakkie.

Fox Mulder (David Duchovny) and Alex Krycek (Nicholas Lea) are summoned to the ensuing hostage situation by Agent Lucy Kazdin (CCH Pounder), since Barry insists that he is an alien abductee. Mulder contacts Dana Scully (Gillian Anderson) for assistance, asking her to look into Barry's history. Mulder acts as a hostage negotiator, calling Barry in order to earn his trust so that the standoff may be peacefully resolved. Barry quickly figures this out, causing Mulder to learn that he is a former FBI agent. A power outage occurs, frightening Barry and causing him to fire his gun, hitting one of the hostages. Mulder heads inside the travel agency with a paramedic. Barry releases the wounded hostage in exchange for Mulder, who is instructed to get Barry near the agency's front door so that snipers can fire on him.

Scully arrives and reveals that Barry's frontal cortex was damaged when he was shot in the head in 1982; she thinks this injury has made Barry a psychopathic pathological liar. Mulder talks to Barry, who claims that the aliens performed painful tests on him and put tracking devices in his body. Against Kazdin's orders, Mulder tells Barry that he believes his story, convincing him to release the remaining hostages. However, when Mulder questions whether Barry is lying, he becomes enraged. Mulder tricks Barry into approaching the front door where he is shot by a sniper.

The next day, Mulder visits Barry in the hospital. Kazdin appears, revealing that metal implants were found in Barry's body and that tiny holes were found in his teeth, in the same manner he had described. Mulder gives one of the implants to Scully, who has it reviewed by a ballistics expert; they find a microscopic barcode imprinted on it. Later, at a supermarket, Scully swipes the implant across a checkout scanner, causing the machine to malfunction while displaying a strange serial number. At her house, Scully leaves a message on Mulder's voicemail, suggesting that Barry had been "catalogued" by the implant. But just then, Barry—having escaped from the hospital—breaks in through Scully's window and kidnaps her.

S2E6 · Ascension

Upon hearing Dana Scully 's (Gillian Anderson) kidnapping by Duane Barry as she leaves a message on his answering machine, Fox Mulder (David Duchovny) heads to her apartment and surveys the crime scene. He meets with her mother, Margaret, who has had a dream about Scully being taken away. The next morning, Assistant Director Walter Skinner tells Mulder that he is "too close" to the case to be involved, and orders Alex Krycek (Nicholas Lea) to escort him home. Meanwhile, Barry speeds down the Blue Ridge Parkway when he is pulled over by a highway patrol officer. When Scully—locked in the trunk—tries to get the officer's attention, Barry kills him. Mulder reviews a video of the traffic stop, and sees that Scully is still alive.

Mulder realizes that Barry is heading to a ski resort at Skyland Mountain, the location of his original abduction; he is attempting to follow through with his original plan of having the aliens abduct someone there in his place. Krycek informs the Smoking Man (William B. Davis) of these findings before departing with Mulder. When they arrive, Mulder boards the resort's aerial tramway in the hopes of reaching the mountain's peak before Barry. However, Krycek tries to delay Mulder by sabotaging the tramway's journey upward. Mulder manages to complete the journey and witnesses a strange light in the area. Upon finding Barry's car, Mulder sees no trace of Scully except her necklace. He then encounters a joyous Barry, who claims that she was taken by "them."

When Mulder interrogates Barry, he becomes so enraged that he nearly strangles him, only to stop himself. When he leaves the room, he orders Krycek to not let anyone inside; however, he finds Krycek talking to Barry when he returns. When Skinner arrives moments later, Barry breaks into convulsions and dies. Later, at the FBI Academy in Quantico, Mulder attempts to question the doctor who performed Barry's autopsy; she refuses to provide details since it was performed by the military instead of the FBI, claiming no other doctors were available.

Krycek meets with the Smoking Man and suggests that they kill Mulder. However, the Smoking Man orders that Mulder be left alive, unless they want to risk "turning one man's religion into a crusade". Mulder and Krycek are ordered to take a polygraph test about Barry's death. A desperate Mulder tries to visit Senator Richard Matheson, only to be discouraged from doing so by his secretive informant, " X " (Steven Williams). In Krycek's car, Mulder finds spent cigarettes from the Smoking Man's meeting with Krycek. Realizing his role in Scully's abduction, Mulder submits a report to Skinner accusing Krycek of impeding his investigation and killing Barry. Skinner summons Krycek to his office, only to learn that he has disappeared. Skinner then announces to Mulder that he is officially re-opening the X-Files.

Mulder meets with Margaret in a park and tries to give her Scully's necklace. Margaret returns the necklace to Mulder, asking that he give it to Scully when he finds her. Margaret also says that she had the dream again about losing her daughter; Mulder takes this as a hopeful sign that Scully may still be alive. A mournful Mulder later returns to Skyland Mountain, to the field where Scully was abducted. Seemingly alone without her, he looks up into the stars.

S2E7 · 3

In Los Angeles, Garrett Lorre, a middle-aged businessman, embarks on a one night stand with an anonymous woman he has met at a corporate party. As they are having sex in his hot tub, the woman bites Lorre to drink his blood. Two other men join the woman, helping her kill Lorre by repeatedly stabbing him using hypodermic needles.

The following day, before departing for L.A., Fox Mulder stores the missing Dana Scully's FBI badge in an X-file under her name. At the crime scene he meets with LAPD detectives investigating the case, explaining that Lorre's murder is the latest in a series of seemingly vampiric serial killings that have spanned two other states. Because the killers write biblical passages in the victims' blood, Mulder believes that they view themselves as an "Unholy Trinity."

Mulder visits a local blood bank where a night watchman has been recently hired. Mulder has him arrested after he is caught drinking blood in the facility's storeroom. During his interrogation, the suspect tells Mulder that he belongs to a trio of vampires who desire immortality; he is known as "The Son" while the other two, a man and a woman, are called "The Father" and "The Unholy Spirit". Mulder does not believe The Son's claims. However, at sunrise, The Son is burned to death when sunlight from the window touches his flesh. Mulder is taken aback, having previously assumed vampires to be purely mythological.

During an examination of The Son's body, Mulder discovers a stamp for Club Tepes, a local vampire club. There, he comes across a young woman named Kristen Kilar, who partakes in the consumption of blood. His suspicion aroused, Mulder follows Kristen after she and another club patron, David Yung, leave for an erotic liaison. He initially fears that Kristen is targeting Yung, but is beaten by Yung when he catches the agent spying on them. After Mulder leaves, Yung is murdered by the two killers, although the reason is not known.

Mulder runs a background check on Kristen, discovering that she formerly lived in Memphis and Portland —both the locations of earlier murders. Mulder assists the LAPD in searching her home, where he finds various blood-related paraphernalia. When she arrives later, Mulder is waiting for her. Kristen tells Mulder that she met The Son in Chicago and that they had engaged in "blood sports" together. Later, she fled The Son as he formed the Unholy Trinity with his accomplices and began their killing spree, following her across the country. Mulder and Kristen soon kiss while The Son, who has returned from the dead, looks on. The next morning, The Son confronts Kristen and tells her that by killing Mulder and drinking the blood of a "believer", she will become one of them.

Kristen approaches Mulder with a knife but instead stabs The Father, who is hiding in the bedroom. The Son attacks Mulder but is subdued. Mulder and Kristen try to escape using a car parked in the garage, but the Unholy Spirit jumps onto the car and attacks Mulder after smashing the windshield. Kristen jumps into the driver's seat and drives into her, impaling her on a wooden peg on the wall. Kristen tricks Mulder into running outside while she goes back into the house and pours gasoline around herself and The Son. Kristen lights a match, blowing up the house and taking her own life in order to kill the other vampires. Firefighters and police find four bodies in the ruins while Mulder stares at Scully's cross necklace.

S2E8 · One Breath

FBI special agent Dana Scully (Gillian Anderson) is currently missing, having disappeared after being kidnapped by a deranged multiple- abductee in the two-part episodes " Duane Barry " and " Ascension ". Her partner Fox Mulder (David Duchovny) has continued his work without her, but is still investigating her disappearance, believing her to have been abducted by aliens. His investigations into similar abductions in the past have been aided by The Lone Gunmen, a trio of conspiracy theorists made up of John Byers (Bruce Harwood), Melvin Frohike (Tom Braidwood) and Richard Langly (Dean Haglund).

Scully's mother, Margaret (Sheila Larken), tells Mulder a story about Dana shooting a snake with her brothers as a child and regretting what she did. She indicates that she is ready to let go of Dana and shows Mulder Scully's gravestone. Mulder, however, refuses to give up.

Scully then turns up mysteriously at a hospital in a coma. An out-of-control Mulder demands to know how she got there and is escorted out by security but calms down and meets with Dr. Daly (Jay Brazeau), who reveals that no one can figure out how she got there or what's wrong with her. At Scully's bedside, Mulder meets her older sister Melissa (Melinda McGraw).

Scully has a vision of sitting in a boat, attached by rope to a dock where Mulder and Melissa stand with the mysterious Nurse Owens behind them. Frohike visits Scully and sneaks out her medical chart, which the Lone Gunmen investigate. Byers finds that Scully's blood contains branched DNA that may have been used for identification but now is inactive and a poisonous waste product in her system.

Later, Mulder visits Scully while another nurse takes her blood. A mysterious man steals Scully's blood sample and runs. Mulder chases him to the parking lot where he is confronted by X, who demands that he stop pursuing what happened to Scully and let her die. X then executes the man who stole her blood. When Assistant Director Walter Skinner (Mitch Pileggi) calls Mulder to his office regarding the incident, Mulder denies any involvement and claims that The Smoking Man is responsible for what happened to Scully. Mulder demands to know where he is, but Skinner refuses to tell him.

In another vision, Scully lies on a table and is visited by her deceased father. Mulder, with Melissa in the hospital cafeteria, is asked by a woman for change for the cigarette machine. When she says that a pack of Morleys is already there and leaves, Mulder opens it and finds the Smoking Man's address inside. Mulder bursts into the Smoking Man's home and holds him at gunpoint, demanding to know why Scully was taken instead of him. The Smoking Man claims he likes both of them, which is why she was returned; he reveals that he told Skinner that Mulder shot the man in the parking lot, although he didn't believe this to be true, incidentally revealing himself as being unaware of who did, namely X. He tells Mulder that he'll never know the truth if he kills him, and Mulder decides not to.

Mulder returns to FBI headquarters and types a resignation letter that he hands to Skinner. Skinner visits his office as Mulder is packing and relates an out-of-body experience he had in Vietnam. He refuses to accept Mulder's resignation, and Mulder realizes that he was the one who provided him with the Smoking Man's location. Heading to the parking garage, Mulder is met by X, telling him that he'll have a chance for revenge that night when men, believing him to have information on Scully, will search his apartment. Mulder is waiting with his gun at his apartment when Melissa arrives. Although he initially refuses to leave, Melissa convinces Mulder to see Scully. While with Scully, Mulder holds her hand and talks to her. Returning home to find his apartment trashed, he sits on the floor and cries.

Scully awakens the following day, and Mulder is called to the hospital to see her, where she indicates that she heard his voice while in her coma, and he returns her cross necklace. Scully tells him she doesn't remember anything after being kidnapped by Duane Barry. Later, Scully asks one of the nurses if she can see Nurse Owens, but the nurse tells Scully that no nurse named Owens has ever worked at that hospital.

S2E9 · Firewalker

Dr. Adam Pierce, a scientist at the California Institute of Technology in Pasadena, intercepts a visual transmission from Firewalker, a mobile robot sent by a volcanic research project on Mount Avalon in the Cascades of Washington State. Firewalker is broadcasting from inside a volcanic cave, where Pierce glimpses the dead body of the chief seismologist, Phil Erickson. He also sees a shadow moving in the cave, an impossibility due to the extremely high temperatures. Firewalker's camera is then destroyed, ending the transmission.

Pierce goes to Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson), showing them a TV interview of the project's leader, Daniel Trepkos (Bradley Whitford); Pierce was with the project until he and Trepkos had a falling-out. Mulder is reluctant to let Scully come along because of her recent abduction; Scully, however, insists that she is ready. Upon arriving at Mount Avalon, Pierce enters the woods to inspect the project's equipment while the agents search the laboratory. They discover the seemingly traumatized team: robotics engineer Jason Ludwig (Leland Orser), systems analyst Peter Tanaka (Hiro Kanagawa), and graduate student Jessie O'Neil (Shawnee Smith). They claim that Trepkos destroyed their lab and disappeared after Firewalker's first descent. Meanwhile, outside, Trepkos strangles Pierce.

After the team retrieves Pierce's body, Mulder reviews Trepkos' fragmented notes. He finds references to a new silicon-based organism existing inside Mount Avalon; Scully, however, doubts his conclusions because of his mental state. Tanaka breaks into convulsions and displays a high fever, but refuses any help from Mulder or Scully. When he is put on a stretcher for a medivac pickup, Mulder notices a throbbing bulge in his neck. Tanaka flees into the woods and dies when a tentacle-like ascocarp bursts out of his throat. An autopsy by Scully finds sand (silicon dioxide) in his lungs, indicating the existence of a silicon-based lifeform; she theorizes that the organism infects the nearest hosts or otherwise dies. Mulder contacts the CDC to have them quarantine the site.

Mulder and Ludwig venture into the volcanic caves to find Trepkos. When they find Firewalker, Trepkos shoots Ludwig in the back with a flare gun, killing him. He then burns Ludwig's body, as he was infected. Trepkos tells Mulder that after Firewalker returned from its first descent, Erickson pulverized a rock in one of its samples, resulting in his death and the infection of all the scientists immediately surrounding him. Trepkos says that the organism is parasitic in nature, making its hosts pass itself on to others. Meanwhile, in the lab, an infected O'Neil handcuffs herself to Scully to expose her to the fungus. Scully protects herself by throwing O'Neil into a sealed chamber and closing the door. The fruiting body breaks out from O'Neil's throat, killing her without spreading the disease any further.

Mulder and Trepkos arrive on the scene. Mulder radios the evacuation team but—knowing that Trepkos will refuse to go—reports that only he and Scully have survived the ordeal. The agents enter a month-long quarantine while the Chemical Corps confiscates the lab and cordons off Mount Avalon. Firewalker is salvaged, but is too damaged to yield sufficient data. Trepkos and O'Neil are officially unaccounted for and presumed dead; Trepkos is last seen carrying O'Neil's body as he disappears into the volcano.

S2E10 · Red Museum

Fox Mulder and Dana Scully are called in to investigate a number of kidnappings in Delta Glen, Wisconsin, where local teenagers have been found half-naked and drugged with either the phrase "He is one" or "She is one" written on their backs. Interviewing a kidnap victim, the agents initially suspect a nearby cult, the Church of the Red Museum, founded by vegetarian named Richard Odin. Mulder, Scully and the local sheriff, Mazeroski, attend a ceremony of the cult, causing Mulder to believe that members of the cult are walk-ins, people whose souls have been taken over by a spirit.

After an altercation between the agents and four teenagers, including the Sheriff's son Rick and Rick's girlfriend Katie, Katie is kidnapped and found the next morning. On examination, her blood is found to contain an unknown alkaloid substance and high levels of scopolamine. Mulder and Scully conclude that only medical personnel would have access to scopolamine, leading them to increasingly suspect Odin, a former doctor. The agents bring Odin in for questioning but are interrupted by a confrontation outside, in which a large group of Red Museum members has blocked access to the local BBQ restaurant.

An old man in a truck leads the agents to two men injecting growth hormone into cattle. The old man believes the tainted beef is making the locals more violent and aggressive. That night, Jerrold Larson, the local doctor, is killed in a plane crash. An investigation turns up evidence that trace back to the kidnapped teens, implicating Larson. Meanwhile, one of the men injecting the cows is murdered by the Crew Cut Man. Mulder and Scully visit Beth, the mother of a kidnapped victim who reveals that Larson was giving her child "vitamin shots." Mulder notices light coming from the bathroom mirror and discovers a hidden room full of videotapes and a camera.

After being abducted from his car, Rick is found dead in a similar fashion as the other kidnapped teens, except with a bullet wound; the Crew Cut Man is seen leaving the area. The agents investigate another resident, Gerd Thomas, on suspicion of Rick's murder and the hidden room. During questioning, Gerd tells Mulder that Larson had been paying him to inoculate the cows with the same "vitamin shots" injected into the children. Convinced that they were turning into monsters, Gerd kidnapped the children and drugged them with scopolamine and psychedelics to make them "pure" again. During the interrogation, Scully recalls and recognizes the Crew Cut Man as the assassin who killed Deep Throat.

A toxicology report reveals the presence of a mysterious substance known as "Purity Control", leading Mulder to theorize that Larson had been injecting the children with alien DNA. He convinces Mazeroski to round up all of the families of Larson's patients, believing their lives to be in danger, and have them hidden at the Church of the Red Museum. Mulder tracks down the Crew Cut Man at a beef processing plant that has been doused with gasoline. The Crew Cut Man locks Mulder in a freezer and lights a match. Scully, Mazeroski and his deputies arrive, interrupting the Crew Cut Man's attempts to destroy the plant. Mazeroski kills the Crew Cut Man in revenge for Rick's murder, to Mulder's dismay.

Scully reports that the Crew Cut Man had no records on file with the FBI or other agencies. The material injected into the cows and children is found to be an unknown substance. All the children who were inoculated came down with a flu -like illness, but those in the Church of the Red Museum, being vegetarians, did not become ill. Scully thinks the Church of the Red Museum may have been used as a control group without their knowledge and declares the case open and unsolved.

S2E11 · Excelsis Dei

FBI agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) are called to the Excelsis Dei nursing home in Worcester, Massachusetts, in order to investigate a nurse's claim that she was raped by an invisible entity. Severely bruised, Michelle Charters (Teryl Rothery) claims that she knows who was responsible and names the attacker as Hal Arden, an elderly resident with Alzheimer's disease. When questioned, Hal admits that he made sexual overtures to Michelle but claims that it was harmless and that he is too elderly to have done anything. In turn, the hospital's administrator believes that Michelle has manufactured the rape allegation in order to extort money from the nursing home.

As Mulder and Scully investigate, they discover that many of the facility's Alzheimer's patients have shown significant improvement over their condition, a development that is not medically possible. Their doctor, Grago, attributes the patients' improvement to regimen he has applied using Deprenyl, an experimental drug that has so far shown negligible effect in patient studies. Before Mulder and Scully can make much headway, Hal dies unexpectedly while his roommate, Stan Phillips, stands by, complicating the investigation further. Worried about her father, Stan's daughter arranges to move him back into her home, despite his angry insistence that he doesn't want to leave. An orderly tries to help Stan pack, but Stan flees the room and leads the orderly on a chase to the roof. The orderly follows Stan out of a window but falls or is pushed to his death before Mulder can save him.

Mulder and Scully eventually discover that a Malaysian orderly, Gung Bittuen, is dosing the patients with an herbal drug made of mushrooms he cultivates in the building's basement. He explains that in Malay culture, the elderly are revered and treated with respect; coming to the U.S., Gung was appalled to see how Westerners send their elderly away to places like Excelsis Dei, where—as Gung has seen firsthand—they are badly mistreated. Gung attempted to ease their suffering with the herbal drug but admits something has gone badly wrong.

While the mushrooms are used in his country to "speak with the dead," the spirits lingering around Excelsis Dei are restless and angry, and the living residents' use of the mushrooms has given the spirits a power to act on that anger. The drug reverses the patients' Alzheimer's symptoms, but also allows them to channel the spirits, resulting in the assaults and murders.

As Stan, who stole all of Gung's herbal stash, overdoses and begins seizing, the spirits once again attack Charters, trapping her and Mulder in a flooding bathroom. Scully and Grago manage to stop Stan's seizures, at which point the spirits disappear and the bathroom door opens, freeing Mulder and Charters. The government of Massachusetts takes over the facility, and Gung is turned over to immigration services. The remaining original patients, no longer having access to the drug, revert to their previous state of dementia.

S2E12 · Aubrey

In the town of Aubrey, Missouri, local detective Betty June "B.J." Morrow tells Lt. Brian Tillman (Terry O'Quinn) that she has gotten pregnant from their affair. Tillman asks B.J. to meet him at a motel later that night. While waiting for him, B.J. has a vision that leads her to a field where she digs up the skeletal remains of an FBI agent.

Agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) head to Aubrey, where the remains are identified as belonging to Agent Sam Chaney, who disappeared in the area with his partner, Tim Ledbetter, in 1942. The agents find discrepancies in B.J.'s story, but Tillman comes to her defense. Mulder tells Scully of the case Chaney and Ledbetter were investigating, which involved the rapes and murders of three women with the word "Sister" slashed on their chest. Discovering similar cuts on Chaney's chest during the autopsy, B.J. instinctively realizes that the cuts spell the word "Brother." B.J. admits her affair and pregnancy to Scully.

Tillman reveals that a new murder has occurred where a woman had the word "Sister" slashed on her chest. B.J. claims to have seen the victim in her dreams, which involve a man with a rash on his face and a monument which, after a quick sketch by B.J., Mulder recognizes as the Trylon and Perisphere from the 1939 New York World's Fair. Searching old mugshot photos, B.J. recognizes the man from her dream as Harry Cokely, who was arrested in 1945 for raping a woman named Linda Thibedeaux and slashing "Sister" on her chest. Scully believes that B.J. subconsciously recalled the case, since her father was a cop and may have discussed it. The agents visit the now-elderly Cokely, who lives alone after being released from prison in 1993. Cokely insists he was at home when the latest murder occurred.

B.J. awakens from a nightmare covered in blood, finding the word "Sister" slashed into her chest, and sees a young Cokely reflected in the mirror behind her. She heads to a stranger's basement and tears away the floorboards, revealing a skeleton that is found to be the remains of Agent Ledbetter. Cokely is arrested, but denies attacking B.J., insisting he's too old to even leave his house without his oxygen flask. Scully tells Mulder that blood on the latest victim matches Cokely's. The agents visit Thibedeaux, who describes her encounter with Cokely in the 1940s.

Mulder notices a photo of her at the 1939 World's Fair. When pressed, Thibedeaux reveals that the rape resulted in a child, which she put up for adoption. The FBI tracks down the child, who turns out to have been B.J.'s father, causing Mulder to surmise that B.J. is the killer and may be operating on genetic memories which tend to skip a generation.

As the agents are on their way to intercept her, B.J. attacks Thibedeaux, but stops when she sees the "Sister" scars on her chest. The agents find Thibedeaux after B.J. has left, and head to Cokely's house, believing him to be her new target. B.J., who has already arrived, cuts Cokely's respirator tubes and attacks him with a razor. As Mulder is looking for them in the house, he is attacked by B.J. She threatens to cut his throat with the razor, at which Scully and Tillman compel her to stop. B.J. finally surrenders after Cokely dies. She is then placed in a female psychiatric ward, where she is put on suicide watch after attempting to self-abort.

S2E13 · Irresistible

In St. Paul, Minnesota, a funeral is held for a young girl. The ceremony is observed by Donnie Pfaster, the eerie assistant director for the funeral home. Later that night, Pfaster's boss catches him cutting off the corpse's hair and promptly fires him.

Fox Mulder and Dana Scully are summoned to Minneapolis by Moe Bocks, an FBI field agent who is investigating the exhumation and desecration of a body in a local cemetery. Mulder discounts Bocks' theory that this act is a variation of extraterrestrial cattle mutilation, and suggests they search for a human culprit. Scully is disturbed at the sight of the disheveled corpse. Two more bodies are found exhumed, with their hair cut and fingernails removed. Mulder develops a psychological profile of the criminal, believing him to be an escalating "death fetishist " who may resort to murder to satisfy his desires. Scully keeps her discomfort with the case to herself, and writes up a field report on necrophilia.

Pfaster, who is behind the exhumations, proves Mulder's prediction correct when he brings a prostitute to his apartment. When the prostitute discovers a collection of funerary wreaths in Pfaster's bedroom, he kills her and removes her fingers. Later, Pfaster—having been hired as a frozen food delivery man—delivers to the low-security house of a woman with teenaged daughters. In the bathroom, he steals some discarded hair from a brush found in the trashcan. Pfaster attends a night class at a community college, where a female classmate defends herself after he makes threatening advances. He is arrested and is placed in a jail cell across from a suspect being interrogated for Pfaster's crimes by Mulder, Scully and Bocks. Pfaster shows interest in Scully, and learns her name from the interrogated suspect. Pfaster is released as his charges are dropped.

Scully is deeply troubled by Pfaster's crimes, and has unsettling dreams and hallucinations about the case. In Washington, she has a counseling session with a social worker, during which she shares her anxiety about the investigation. After the session, Scully learns that someone from Minnesota had called for her. When she contacts Mulder, she learns that neither he nor Bocks made the call. Tracing a fingerprint to Pfaster from his arrest, Mulder and Bocks raid his apartment, finding one of the prostitute's fingers in his refrigerator. After Scully arrives in Minneapolis, Pfaster forces her car off the road. He kidnaps Scully and takes her to his late mother's abandoned house. He ties and gags Scully, and keeps her in a dark closet.

Mulder and Bocks discover that Pfaster's mother had owned a car which matches paint found on Scully's abandoned vehicle, and track down her former residence. Meanwhile, Scully escapes from Pfaster as he prepares a cold bath for her, resulting in a pursuit through the house. Scully and Pfaster have a struggle that sends them falling down a staircase into the foyer, where a task force led by Mulder and Bocks breaks in moments later and apprehends Pfaster. Scully initially insists that she is okay, but then breaks down and cries in Mulder's arms. In a voice-over narration, Mulder traces Pfaster's pathology to his childhood, when he was raised in a family of four older sisters. Mulder also reflects on Pfaster's nature and the nature of evil in general.

S2E14 · Die Hand die Verletzt

In Milford Haven, New Hampshire, a group of high school faculty members meet to discuss various social events. The adults initially appear to be socially conservative, debating the suitability of letting students perform Jesus Christ Superstar. However, when the group ends the meeting in a prayer, they recite a Satanic chant.

Later, a group of students venture into the woods at night to play with black magic, an attempt to "score" on the part of the boys in the group. The experiment causes unexplainable things to happen, and all but one of the teenagers flee. The remaining teen's mutilated body is discovered the next day, leading Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) to investigate. Locals—including the Satanists—claim that the teens have unleashed a demonic force with their rituals. This theory is given validity by strange occurrences, such as frogs falling from the sky and water in the drinking fountain draining counter-clockwise, contrary to the Coriolis effect.

Unknown to the agents, substitute teacher Mrs. Phyllis Paddock (Susan Blommaert) is behind the murder, keeping the eyes and heart of the victim in her desk. One of the faculty members, Jim Ausbury (Dan Butler), suspects one of the other Satanists killed the teen, but they believe it was an outside force.

While dissecting a pig fetus in science class, Ausbury's stepdaughter, Shannon (Heather McComb), suffers a breakdown when she hallucinates the cadaver as alive. Meeting with Mulder and Scully, she tearfully tells them that Ausbury and the other Satanists repeatedly raped and impregnated her during their rituals, sacrificing her babies. A shocked Ausbury denies the accusations. Shannon stays after school to make up her assignment of dissecting the pig. Paddock takes her bracelet and uses it as part of a spell that causes Shannon to slit her wrists.

When Ausbury learns that the Satanists plan to use Shannon as a scapegoat, he admits the sect's existence to Mulder. He confirms that rituals did happen while Shannon was present, but insists that exposure to sensational media coverage led her to "remember" the alleged sexual abuse. Meanwhile, Scully researches Paddock and finds that no one knows anything about her or her background. During a sudden power outage, Paddock steals Scully's pen and uses it to impersonate her in a call to Mulder, pretending to be in trouble. Mulder handcuffs Ausbury in his basement to prevent his possible escape, then leaves to help Scully. Soon after, a giant snake appears, controlled by Paddock, and devours Ausbury.

Mulder finds out that Scully never called him. The two find Paddock seemingly attacked by the remaining Satanists, and go to search for them. The Satanists capture the two agents, convinced that they need to perform a sacrifice to regain favor with the Devil and make up for their faltered faith. As they are about to kill Mulder and Scully, Paddock causes them to instead kill themselves, confirming that their attempt was too late. The agents escape their bonds and find Paddock missing, with only a parting message on the chalkboard stating, "Goodbye. It's been nice working with you."

S2E15 · Fresh Bones

In Folkstone, North Carolina, Jack McAlpin, an agitated Marine Corps private, drives his car into a tree after several hallucinatory episodes and is apparently killed. On the tree is a veve, a drawn voodoo religious symbol.

McAlpin is the second purported suicide among troops stationed at an Immigration and Naturalization Service compound processing refugees from Haiti. Fox Mulder and Dana Scully visit the compound to investigate McAlpin's death. There, a young boy named Chester Bonaparte sells a good luck charm to Mulder. After meeting with Colonel Wharton, the head of the compound, Mulder interviews an imprisoned refugee, Pierre Bauvais, and an associate of McAlpin's, Harry Dunham. When Scully attempts to perform an autopsy on McAlpin's body, she finds a dog carcass in its place at the morgue.

While driving down the road, Mulder and Scully discover a still-living McAlpin, who doesn't remember what has happened to him. Tetrodotoxin, a chemical Mulder believes is part of Haitian zombification rituals, is found in McAlpin's blood. The agents go to the local graveyard to investigate the corpse of the other dead soldier, but find the grave robbed. They also find Chester, who collects frogs at the cemetery and sells them to Bauvais. Dunham approaches Mulder, telling him that Wharton has begun abusing the refugees as a means of retaliation against Bauvais; Wharton denies the accusations, but later has Bauvais beaten to death.

Scully cuts her hand on the thorn of a twig left in her car. When she drives off, a veve is seen on the ground under the car. Mulder has a meeting with X, who tells him that he and Scully will soon be called back to Washington and that the camp will be restricted to military personnel only. Mulder believes Wharton is persecuting the refugees after the suicide of some of his men during a previous trip to Haiti. Scully finds Dunham dead in a bathtub, and Mulder catches McAlpin with a knife nearby. Although he has no recollection of the event, McAlpin confesses to be the murderer under the influence of Wharton, who tells the agents that Bauvais committed suicide and that their investigation is over.

McAlpin's wife provides the agents with a photo of Wharton with Bauvais in Haiti, causing the agents to go through his office. They find that both Dunham and McAlpin had filed complaints against Wharton over his treatment of the detainees. The agents head to the cemetery, where Wharton is performing a voodoo rite over Bauvais' coffin. When Mulder confronts him, Wharton harms him through sympathetic magic. Meanwhile, in a hallucinatory episode, a man emerges from the small cut in Scully's hand and strangles her, but the illusion disappears when she grabs the charm Chester sold them. Bauvais appears and stops Wharton by blowing tetrodotoxin in his face. Scully arrives to assist Mulder and pronounces Wharton dead. Scully opens Bauvais' coffin and finds his body still intact.

The next day, the agents say goodbye to McAlpin, who reveals that Chester was a boy who had died in a riot six weeks earlier. The episode ends with Wharton being unwittingly buried alive by the graveyard watchman.

S2E16 · Colony

The episode opens in medias res with Fox Mulder in a field hospital in the Arctic. As Mulder is lowered into a tub of water, Dana Scully bursts in and tells the doctors that the cold is the only thing keeping him alive. Suddenly, Mulder's heart monitor flatlines.

Two weeks earlier, in the Beaufort Sea, crewmen on a ship spot a light in the sky that soon crashes into the water. A body is retrieved from the crash, revealed to be an Alien Bounty Hunter. Two days later, the Bounty Hunter arrives at an abortion clinic in Scranton, Pennsylvania, and kills a doctor by stabbing him in the back of the neck with a stiletto weapon, then sets the building on fire and escapes. Mulder receives emails containing the doctor's obituary along with two other identical doctors. After interviewing a pro-life priest who had threatened one of the doctors, they go to a newspaper office in Binghamton, New York, and use a classified ad looking for one of the men to track another one, Aaron Baker, to Syracuse.

Mulder has a fellow FBI agent, Barrett Weiss, visit Baker's residence. Weiss and Baker are both killed by the Bounty Hunter, who impersonates Weiss and tells Mulder and Scully that no one is home. After Walter Skinner hears of Weiss' death and closes the case, the agents meet CIA official Ambrose Chapel, who tells them that the doctors are clones from a Soviet genetics program and are being systematically killed by both the Russian and U.S. governments. Mulder, Scully and Chapel head to pick up another doctor named James Dickens, but Dickens flees at the sight of Chapel, who is really the disguised Bounty Hunter. Dickens is killed by the Bounty Hunter in the subsequent pursuit, unknowingly aided by Mulder and Scully.

Scully doubts "Chapel's" credibility, but Mulder believes his story due to his credentials and experience. Scully performs an autopsy on Weiss and finds that his blood has coagulated, while his red blood cell count is excessively high. Scully finds an address on a bag recovered from Dickens' residence and heads there, discovering a lab that is in the process of being destroyed by "Chapel." Meanwhile, Mulder is summoned to the home of his father, Bill, and learns that his sister Samantha has seemingly returned home after being abducted decades before. Samantha claims that she was returned around age nine with no memory, and recently recalled her experience through hypnosis.

Samantha tells Mulder that the Bounty Hunter and the clones are actually aliens, and the Bounty Hunter will begin chasing her as soon as he has killed the remaining clones. Meanwhile, Scully heads to a hotel to hide from the Bounty Hunter. Returning to the lab, she finds four more clones, who claim to be the last. Scully arranges for them to be transported to a safe place, but the Bounty Hunter follows her and watches. The four clones are taken to a federal stockade, where they are killed by the Bounty Hunter, disguised as a prison official. At her hotel room, Scully lets in a man who seems to be Mulder, only to receive a phone call from the actual Mulder soon after.

S2E17 · End Game

USS Allegiance, an American nuclear submarine, is patrolling the Beaufort Sea off the coast of Alaska when it comes across a craft below the ice that is emitting a radio signal. Allegiance is ordered to fire upon the craft by Pacific Command. However, the craft manages to disable the sub using a high-pitched frequency, stranding it below the ice.

Continuing from the cliffhanger ending of " Colony ", Dana Scully (Gillian Anderson) is beaten and kidnapped by "Mulder", who is really the Alien Bounty Hunter in disguise. When the real Mulder (David Duchovny) finds the wrecked hotel room, his sister Samantha explains that the Bounty Hunter will set up a hostage exchange to swap Scully for her. She further explains that the Bounty Hunter can only be killed by piercing the base of his neck and that his alien blood is deadly to humans. Finally, Samantha reveals that the clones are the progeny of two original aliens and worked at abortion clinics to gain access to fetal tissue. Their objective was to set up an extraterrestrial colony on Earth, an effort that has gone as far back as the 1940s. Because the clones' experiments were considered to have tainted their alien race, the Bounty Hunter was sent to kill them.

Walter Skinner meets Mulder and Samantha at Mulder's apartment, telling them that the remaining clones are missing. Mulder receives a call from Scully, who tells him that the Bounty Hunter seeks an exchange for Samantha. Mulder and Samantha are sent to a bridge near Bethesda while Skinner hides nearby with a sharpshooter. After the exchange takes place, Samantha attacks the Bounty Hunter. During the struggle, the sharpshooter fires upon the Bounty Hunter, and both he and Samantha fall into a river. An anguished Mulder tearfully apologizes to his father, Bill, for losing her again.

Bill leaves Mulder a note from Samantha, which provides him with the address of a Maryland clinic where they can meet if separated. Mulder hopes that she is alive, but soon gets a call from Scully reporting that Samantha's body has been found. After Scully ends the call, she discovers Samantha's body dissolving into a green liquid.

Meanwhile, inside the clinic, Mulder finds multiple clones of Samantha working on fetuses in labs similar to that of the clones. They reveal that they manipulated Mulder by sending one of their own to pose as "Samantha" in an effort to have him protect her original clone. They claim to know the real Samantha's location. Mulder, realizing he has been duped, initially refuses to help and starts to leave, but is knocked unconscious by the Bounty Hunter, who proceeds to kill the Samantha clones and burn down the clinic. When no trace of the clones is found, Mulder meets with X at the Kennedy Center, demanding to know the Bounty Hunter's location.

X says that the Bounty Hunter's craft below the Beaufort Sea has been found, and that a naval fleet has been sent to destroy it. Mulder heads there and e-mails Scully to tell her not to follow him.

Scully goes to Skinner for help, but he initially refuses. She summons X to Mulder's apartment, but he turns her down. On his way out, X is confronted by Skinner in an elevator. After the two men engage in a vicious physical altercation, X divulges Mulder's whereabouts. Meanwhile, Mulder finds the stranded Allegiance, with its sail broken through a patch of shallow Arctic ice. Inside, he finds what seems to be the sub's only surviving crewman, whom Mulder realizes is the disguised Bounty Hunter. The two struggle, during which Mulder becomes exposed to the Bounty Hunter's toxic blood.

The Bounty Hunter claims that Samantha is still alive before dumping Mulder off the sail and submerging Allegiance; a weak Mulder is nearly cut in half with the sub's diving plane in the process. He is discovered and rushed to the field hospital seen at the beginning of "Colony", where Scully—having learned that the alien blood contains a retrovirus that dies in cold temperatures—convinces the doctors to take him out of the bath that would warm up his body.

As Mulder's condition stabilizes, Scully writes a field report crediting science with detecting the retrovirus and saving Mulder. She contends that the retrovirus is of a mysterious origin, and reports that neither the Bounty Hunter nor Allegiance have been found. When Mulder regains consciousness, he tells Scully that his experiences did not give him the answers he had been searching for, but that they have given him renewed "faith to keep looking".

S2E18 · Fearful Symmetry

In Fairfield, Idaho, two janitors witness an invisible force storm down a city street; a road worker is later killed by the force on the highway. The next day, an elephant suddenly materializes in front of an oncoming big rig. The driver manages to stop in time, but the elephant soon collapses and dies, over forty miles away from where it disappeared the night before at the Fairfield Zoo.

Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) survey the damage in the city, which appears to have been caused by an elephant even though none was seen. Ed Meecham, an animal handler at the zoo, recounts how he came to the elephant's locked cage to find it empty. His boss, Willa Ambrose, tells the agents that the zoo is in danger of closing due to other animal disappearances. She blames the zoo's decline on an animal rights group which is known to free captive animals. The group's leader, Kyle Lang, denies any involvement in the elephant's release. Lang tells them that Ambrose is being sued by the Malawi government over a lowland gorilla she took from their country ten years prior.

Mulder contacts Frohike and Byers, who say that Fairfield is known for its animal disappearances and UFO sightings. They also mention Ambrose's gorilla, who is known to communicate using American Sign Language. Meanwhile, Scully follows one of Lang's activists as he sneaks into the zoo, running into Meecham inside. The activist attempts to free a tiger, but after a flash of light, the tiger seemingly disappears. The activist is promptly mauled to death, with the killing captured on his night vision camera. When questioned, Lang denies any responsibility for the death. Ambrose introduces the agents to the gorilla, Sophie, who has been cowering in her cage and expresses an apparent fear of light.

Scully performs a necropsy on the elephant, revealing it to be pregnant — which is impossible, since the animal had never been mated. The tiger reappears at a Boise construction site, and is shot dead by Meecham when it charges at Ambrose; the zoo is shut down the next day over the incident. Mulder tells Ambrose that the tiger was also pregnant, and explains his theory that extraterrestrial aliens are impregnating all the female endangered animals as part of "their own Noah's Ark." Mulder thinks that Sophie too is pregnant and that she is worried that her baby will be abducted. Sophie confirms Mulder's suspicions when she makes signs for "baby go flying light".

Sheriff's deputies order Ambrose to release Sophie into protective custody, presumably to be sent back to Malawi. Ambrose unsuccessfully seeks help from Lang, her former boyfriend, but he advises to let Sophie return to the wild. Lang later goes to see Ambrose at the warehouse where Sophie is being prepped for shipping, but finds her cage empty. He is then mysteriously killed by a falling crate. Scully finds that Lang was struck with a cattle prod and suspects Ambrose of killing him, but she claims that Meecham is responsible. Mulder goes to arrest Meecham, who is keeping an angered Sophie at another warehouse near Boise. Meecham suddenly locks Mulder in Sophie's room, where the enraged gorilla attacks and injures him.

A bright light appears and causes Sophie to vanish, but not before she gives Mulder a final message in sign language. When Mulder gives the message to Ambrose the next day, she says it means "man save man." Ambrose and the agents are then called to the highway, where Sophie has been struck by a car and killed. Ambrose and Meecham are both charged with manslaughter for Lang's death. As the agents leave Idaho, Mulder says through narration that he believes alien conservationists were behind the events in Fairfield.

S2E19 · Død Kalm

In the Norwegian Sea, chaos erupts on board USS Ardent, an American destroyer escort. Due to mysterious and unspecified events, half of Ardent' s crew board lifeboats and abandon ship against the captain's orders. Eighteen hours later, they are spotted by a Canadian fishing vessel; however, in that short span of time, the young crew members have undergone rapid aging.

Dana Scully (Gillian Anderson) is asked by Fox Mulder (David Duchovny) to visit the ship's sole surviving crew member, Lt. Harper, who has been quarantined at the Bethesda Naval Hospital. She finds that Harper, despite being in his twenties, has inexplicably aged to the point of being unrecognizable before she is escorted from the room. Mulder explains that Ardent vanished at the 65th parallel, a location with a history of ship disappearances. Mulder believes that a "wrinkle in time" exists there, and that Ardent was the subject of government experimentation related to the Philadelphia Experiment from World War II.

In Norway, Mulder and Scully hire Henry Trondheim (John Savage), a naval trawler captain, to take them to Ardent' s last known location. After crashing into the bow of Ardent, Mulder, Scully and Trondheim find signs of advanced corrosion, even though the warship is only a few years old. Below decks, the party finds the mummified remains of several crew members. They also find the wizened commanding officer of Ardent, Captain Barclay, who claims that "time got lost" after his ship encountered a "glowing light" in the ocean. Trondheim's boat is stolen, and his first mate is murdered.

Trondheim is attacked by a Norwegian pirate whaler named Olafsson, who has not aged despite being on the ship for the past two days. Mulder, Scully and Trondheim eventually begin to age unnaturally. Scully develops a theory that Ardent is sailing near a metallic object beneath the ocean, and that it has caused free radicals to rapidly oxidize their bodies. When Mulder notices that the ship's sewage pipe is the only one not corroded through, the agents realize that something from the ocean contaminated Ardent ' s potable water and led to the aging; Olafsson and his men remained unaffected due to their consumption of recycled water from the sewage system. Desperate to survive, Trondheim kills Olafsson after he reveals the secret and sets out to keep the water for himself.

Scully learns from blood tests that the contaminated water causes rapid oxidative damage and dramatically increases sodium chloride in the body. She tries to ration the drinkable water amongst the three but discovers Trondheim attempting to hoard what little that remains. Trondheim locks himself in the sewage hold, forcing Scully to use minuscule supplies to keep Mulder alive. The mysterious oxidant eventually eats through Ardent ' s hull, flooding the sewage hold and drowning Trondheim. The agents both lose consciousness shortly before Navy rescuers arrive at the ship. Scully comes to at the hospital, where she is told that her written observations on the case helped naval doctors reverse their aging and save Mulder from near-certain death. Scully says that she wants to return to Ardent for more research, but the doctor tells her that the ship sank shortly after their rescue due to the flooding.

S2E20 · Humbug

In the town of Gibsonton, Florida, two brothers are playing in their outdoor swimming pool. A mysterious figure approaches them from the woods and jumps into the pool without their noticing. As the brothers play, they notice something is wrong. The figure emerges from the water; it's revealed to be the boys' father, a freak show act named the "Alligator Man", who scares his sons for fun. After the boys leave the pool for bed, their father stays behind to swim. Another mysterious figure approaches the pool from the woods. It attacks and kills the "Alligator Man" in his pool.

Agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) travel to Gibsonton to investigate a 28-year series of attacks by an unknown assailant in a community of former freak show performers. They attend the funeral of the "Alligator Man" (who suffered from ichthyosis). Among the people they meet afterwards are "self-made freaks" Dr. Blockhead (Jim Rose) and his " geek " sidekick, The Conundrum (The Enigma), who will eat anything but says nothing. The agents also meet former performer Jim Jim, the " Dogface Boy", who later became the local sheriff after his face went through hair loss.

Mulder and Scully stay at the Gulf Breeze trailer court. Here, they meet the distrustful manager Mr. Nutt (Michael J. Anderson), a dwarf, and Lanny (Vincent Schiavelli), an alcoholic with an underdeveloped conjoined twin named Leonard. The agents hear a story about the legendary Fiji mermaid, a common sideshow act in the 19th century that generally turned out to be a monkey with a fish tail attached — the " humbug " referred to by the episode's title. Despite Scully's usual skepticism, Mulder is intrigued because of what look like simian tracks left by the mystery attacker.

One night, Mr. Nutt is fatally attacked by the creature, who the agents eventually discover is Lanny's twin, Leonard, who is able to detach himself from Lanny's body. According to Lanny, Leonard attacks people and attempts to burrow into them because he is looking for a new brother to replace Lanny, who is dying from liver failure. Lanny voluntarily locks himself in the local jail in an effort to keep Leonard from escaping, but dies during the night. Leonard slips through the bars on the cell window and flees. Mulder and Scully try to capture Leonard, who goes inside a funhouse, but he seemingly manages to get away.

Upon leaving the funhouse, the agents find The Conundrum lying on the ground, rubbing his stomach, apparently having been attacked by Leonard. As Dr. Blockhead prepares to leave town with The Conundrum the following morning, he comments to Scully that with modern science eradicating genetic anomalies, it will be up to self-made freaks like him to remind people that "nature abhors normality." The Conundrum looks unwell and Mulder asks what the matter is. The Conundrum — in his only line of the episode — replies, "Probably something I ate." As Dr. Blockhead drives away with The Conundrum, Mulder and Scully turn to each other with confused and somewhat shocked expressions.

S2E21 · The Calusari

In Murray, Virginia, Maggie (Helene Clarkson) and Steve Holvey (Ric Reid) visit an amusement park with their children. During the outing, Teddy, the youngest child, loses his balloon. His father, Steve, substitutes it with Charlie's balloon. In a tragic turn of events, Teddy follows the balloon onto the tracks and is fatally struck by a train. Strangely, Charlie appears unaffected by Teddy's death.

Three months later, Fox Mulder (David Duchovny) shows Dana Scully (Gillian Anderson) a photo taken moments before Teddy's death that suggests a mysterious force lured Teddy onto the tracks. The agents later visit the Holveys, and Scully grows suspicious of Maggie's elderly Romanian mother, Golda (Lilyan Chauvin), who is seen drawing a swastika on the boy's hand. Scully hypothesizes that the Holvey children may be victims of Munchausen by proxy, perpetrated by their grandmother. As they delve deeper into the case, Steve recalls odd occurrences surrounding Golda's arrival after Teddy's birth. Concerned for Charlie's safety, Scully suggests involving the social worker named Karen Kosseff (Christine Willes). However, tragedy strikes when Steve is accidentally killed in his garage, and when the police investigate his death, they discover evidence of ritualistic sacrifices in Golda's room.

In her room, Golda initiates a ritual with several Căluşari mystics. In the meantime, Kosseff shows up at the Holveys' house and asks to meet with Charlie. Suddenly the boy begins to convulse. After noticing smoke billowing out from under Golda's door, Kosseff and Maggie interrupt the ritual. This, however, leads to Golda's demise at Charlie's hands. Kosseff rushes off and finds Mulder, who in turn questions the Căluşari mystics. They explain that their ritual was an attempt to stop "an ancient and unrelenting evil". Kosseff later sits Charlie down and inquires about the struggle, but the boy swears that it was not him in his grandmother's room, but rather another boy named "Michael".

Maggie later tells Mulder and Scully that Michael was the name of Charlie's twin brother who was a stillborn. Terrified, she insists that she and Steve never told Charlie. After Charlie was born, Golda tried to perform a ritual that would have separated the spirits of the two boys. However, Steve would not allow it.

Charlie seizes again and is taken to a hospital. However, Michael pretends to be Charlie and convinces Maggie to take him home. Scully witnesses what is happening, and informs Mulder, who is certain that the spirit of Michael, and not Charlie, is killing people. The two agents split up: Mulder tracks down the Căluşari mystics to complete the ritual, and Scully goes to Maggie's home to protect her. Although Michael very nearly kills Scully and Maggie, Mulder and the Căluşari manage to complete the ritual, which causes Michael's spirit to disappear. Maggie then returns to the hospital and is reunited with Charlie.

S2E22 · F. Emasculata

In the Costa Rican rainforest, entomologist Robert Torrance discovers a decomposing boar carcass covered with purple pustules. While examining one, it bursts, spraying him with fluid. By nightfall, Torrance develops similar boils and attempts to radio for help. When soldiers arrive the next morning, Torrance is dead.

Simultaneously, in Dinwiddie County, Virginia, a prison inmate also named Robert Torrance receives a package containing an infected leg of meat. A pustule on the meat erupts, and Torrance dies within thirty-six hours. Two other inmates, Paul and Steve, clean Torrance's cell but escape in a laundry cart. Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) are sent to help the U.S. Marshals find them. The agents are surprised when the prison is quarantined by the CDC and the National Guard: Mulder decides to join the Marshals to hunt the fugitives while Scully investigates the prison.

Scully discovers that the prison population is infected with a lethal contagion. She finds a pile of body bags ready for incineration and examines Torrance's corpse. Dr. Osbourne from the CDC tries to stop her, but a pustule on Torrance's body erupts in his face. Scully traces Torrance's package to Pinck Pharmaceuticals, a major drug developer, and finds an insect in another prisoner's body. Dr. Osbourne, now visibly infected, reveals that his team works for Pinck and is researching a dilating enzyme produced by the insect. The insect has a parasitic life cycle that kills its hosts. Osbourne claims that Pinck deliberately introduced the insect and contagion into the prison as an experiment. He soon dies, and his body is burned.

Meanwhile, the fugitives murder a man, steal his campervan, and stop at a gas station. Paul calls his girlfriend, Elizabeth, for shelter. They knock out the gas station clerk and escape in his car, evading the Marshals. Mulder witnesses a CDC biohazard team taking the clerk away. Scully warns Mulder that the contagion could spread if the fugitives are not captured. The fugitives reach Elizabeth's house, where she tends to Steve, who is in the late stages of infection. As Steve dies, a pustule erupts in Elizabeth's face, infecting her.

Mulder and the Marshals raid the house, and while they manage to arrest Elizabeth, Paul escapes. Mulder therefore decides to confront Skinner and The Smoking Man, suspecting he and Scully were deceived into taking the case. Mulder argues that the public should know the truth of the situation, but the Smoking Man argues it would cause mass panic, which Scully agrees with.

Questioning Elizabeth, Mulder learns Paul plans to flee to Toronto by bus. Mulder and the Marshals track down the bus and surround it. Mulder persuades a panicking Paul to release a teenage hostage, but before Paul can divulge any information, he is shot dead by the Marshals. Later, Scully explains that Pinck sent the package to a namesake of the dead entomologist to disguise their wrongdoing as a postal error. Mulder confronts Skinner in his office, determined to go public. Skinner, however, warns him they lack evidence, and he tells Mulder to be more cautious in future cases.

S2E23 · Soft Light

At a hotel in Richmond, Virginia, Chester Ray Banton (Tony Shalhoub) reaches a room and frantically knocks on the door while shouting the name ″Morris″. Banton's shouts attract the attention of Patrick Newirth, a guest in the room across the hall. When Newirth looks through his door's peephole, Banton steps back, causing his shadow to slip beneath Newirth's door. Newirth suddenly evaporates, leaving a strange burn mark on the floor. Banton realizes what has happened and flees the scene.

The case of Newirth's death, the latest in several of its kind, is assigned to local detective Kelly Ryan (Kate Twa). She seeks help from Dana Scully (Gillian Anderson), her former instructor at the FBI Academy. Fox Mulder (David Duchovny) also takes part in the investigation, believing Newirth died from spontaneous human combustion. While searching the home of an earlier victim, the agents realize that both she and Newirth had recently traveled by train. Meanwhile, Banton sits in a train station, cautiously looking at the floor; because the room is lit by soft light, his shadow cannot be seen. After he leaves, Banton is confronted by two policemen patrolling the area. Despite Banton's warnings, the officers step into his shadow and disappear, leaving more burn marks.

The following day, while reviewing the station's surveillance tapes, Mulder sees footage of Banton staring at the floor. After blowing up the frame, Mulder sees the logo for a company called Polarity Magnetics on Banton's jacket. At Polarity Magnetics, the agents meet scientist Christopher Davey (Kevin McNulty), who identifies Banton, a physicist conducting research into dark matter. Davey reveals that Banton disappeared five weeks earlier after an incident in his laboratory in which he was locked in a target room with an active particle accelerator and exposed to a large amount of subatomic particles. His account is enough for Scully to consider spontaneous human combustion, but Mulder is now doubtful of this theory.

The agents find Banton at the train station, but he runs to a poorly lit area. He indicates that walking into his shadow will kill the agents, so Mulder shoots out the overhead lights. Banton allows himself to be taken to a mental hospital, where he is put in a room with soft light per his own request. He tells the agents that the accident in his lab caused his shadow to behave like a black hole, splitting atoms into component particles and reducing matter into pure energy. Banton claims that the deaths were all accidents, and that the government wants to exploit him.

Ryan and her superior stop the questioning and declare the case closed, despite Mulder's objections. Mulder contacts X (Steven Williams), who assures him that the government has no interest in Banton. However, X and two associates later attempt to remove Banton from the hospital by cutting the power. In the process, X's associates are killed when the emergency lights turn on and Banton's shadow falls upon them. Banton flees from the hospital.

Banton returns to Polarity Magnetics and is confronted by Ryan, whom he reluctantly kills with his shadow when she tries to arrest him. Banton orders Davey to destroy him with the particle accelerator, but Davey reveals that he has been helping the government hunt him down. Davey locks Banton in with the particle accelerator, but is shot by X. Mulder and Scully arrive soon after, seemingly too late to save Banton from being vaporized by the accelerator; Mulder realizes that X has betrayed him, and tells X to never contact him again. The case is considered closed, but Mulder notes that Davey disappeared after the incidents. At a research facility, X watches as experiments are being performed on a despairing Banton.

S2E24 · Our Town

In Dudley, Arkansas, government health inspector George Kearns follows his seemingly young lover, Paula Gray, into the woods. However, after losing track of Paula, Kearns finds himself surrounded by approaching lights in the woods. He is then killed by an axe-wielding assailant wearing a tribal mask.

When Kearns is reported missing and a witness claims to have seen foxfire near Dudley, Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) investigate. At the site of the alleged foxfire, the agents find the ground burnt. After visiting Kearns' wife Doris, the agents discover that he was about to recommend a local chicken plant, Chaco Chicken, to be closed down for health violations. While giving the agents a tour of the plant, floor manager Jess Harold claims that Kearns had a vendetta against Chaco Chicken. After hearing this, a hallucinating Paula, who works at the plant, grabs and holds Harold at knifepoint. Mulder and Scully attempt to reason with Paula until she is shot and killed by Arens, the local sheriff. The plant's physician, Dr. Vance Randolph, later claims that Paula was suffering from consistent headaches, which Kearns had also reported.

The agents meet Walter Chaco, Paula's grandfather and the plant's owner, who allows the agents to perform an autopsy. The agents find that while Paula's personnel file gives her age as 47, she appears no older than her mid-20s. They also discover that Paula suffered from Creutzfeldt–Jakob disease, a rare and fatal illness that causes dementia. When the agents nearly collide with a Chaco Chicken truck, they learn that the driver also suffered from the disease. Noticing the plant's blood-red runoff in a nearby stream, Mulder orders a reluctant Sheriff Arens to dredge it.

They quickly find the bones of nine people, including Kearns. While inspecting the remains, the agents notice that the skulls are missing and that the bones appear to have been boiled. Meanwhile, Randolph and Harold discuss the uncovered bones and the increase of Creutzfeldt–Jakob cases. When Randolph complains about Chaco's inaction, Harold assures him that he will talk to Chaco.

Using FBI records, Mulder and Scully find that eighty-seven people have vanished within a two-hundred mile radius of Dudley over the past half-century. Mulder suspects that the town's residents are practicing cannibalism in order to prolong life, possibly explaining Paula's youthful appearance. Mulder discovers that Kearns had Creutzfeldt–Jakob disease, and deduces that the other residents caught the illness after consuming his body. The agents try to search the town's birth records for confirmation of Paula's age, but find that they have been destroyed. At Chaco's mansion, Chaco and Harold meet with Doris, who tearfully implies that she "helped" Chaco kill her husband; Chaco instructs her to obstruct the FBI's investigation.

Doris calls Mulder, believing that Chaco wants to kill her; after she hangs up, she is attacked by the masked figure. Scully goes to help Doris while Mulder searches for Chaco at his mansion. There, he finds the shrunken heads of Kearns and other victims in a cabinet. Mulder calls Scully on the phone and hears her being knocked out by Chaco. She is bound and gagged and taken to a secluded field, where Harold has started a bonfire and led the townsfolk in consuming Doris. Chaco berates them for killing one of their own, but Harold chastises him for allowing the Creutzfeldt–Jakob epidemic to occur and has Chaco executed by the masked figure. Scully is about to be killed when Mulder arrives and shoots the figure; he is revealed to be Sheriff Arens. Harold tries to shoot Mulder, but is trampled to death by the fleeing townsfolk.

In narration, Scully explains that Chaco's plant has been closed down by the USDA, and that twenty-seven Dudley residents have died from Creutzfeldt–Jakob disease. She reveals that Chaco was ninety-three years old at the time of his death, and had spent time with the allegedly cannibalistic "Jale tribe" after his transport plane was shot down over New Guinea during World War II. She also states that his remains have never been found; the final scene suggests that Chaco's remains are being fed to chickens at his plant.

S2E25 · Anasazi

In the desert on a Navajo Indian reservation in New Mexico, a teenage boy comes across a boxcar buried in the ground. He retrieves the corpse of an alien-like figure from the boxcar, which he takes back to the reservation and presents to the residents, including a Navajo elder named Albert Hosteen.

Shortly afterward, Kenneth Soona, a computer hacker known as "The Thinker", breaks into the Defense Department database and downloads secret files related to extraterrestrial life, putting them onto a digital tape. When the Syndicate, a secretive group of government officials, learns of the breach, the Smoking Man tells them that he has already resolved the matter, although this is a lie. The Lone Gunmen visit Mulder and inform him that Soona wants to meet with him, but are interrupted by the sound of a gunshot. When Mulder goes out to his apartment hallway to investigate, he finds that one of his neighbors has shot her husband.

Soona gives the digital tape to Mulder at a discreet meeting in a park. An excited Mulder returns to FBI headquarters, only to find that the tape is encrypted. Scully believes the encryption is based on the Navajo language and takes the tape in order to investigate. When Skinner calls Mulder to his office to question him about the tape, Mulder voices his disdain for recent case assignments and his personal belief he has recently been used to “do the government’s dirty work”. The confrontation escalates to the point where Mulder assaults Skinner. Scully is brought before an FBI panel led by Skinner and is questioned about Mulder's actions. Scully is told that Mulder faces dismissal from the FBI, and that she will suffer a similar punishment if she has lied to them.

On Martha's Vineyard, the Smoking Man visits Mulder's father, Bill, and informs him of his son's likely possession of the tape. Scully meets with a Navajo translator, who refers her to a code talker. Mulder is called away to see Bill; when Scully arrives at his apartment, she is grazed by a bullet shot through his window. When Mulder arrives at Bill's residence, his father prepares to reveal the truth about everything, but is shot and mortally wounded by Alex Krycek. When Mulder contacts Scully, she tells him to flee the scene. After Mulder arrives at her apartment, Scully takes his gun from him while he sleeps.

Scully brings the gun to the FBI for comparison against the bullet that killed Bill. When Mulder awakens, he becomes angry and suspicious towards Scully. Returning to Mulder's apartment, Scully finds his water is contaminated. As Mulder enters his building, he spots Krycek, whom he disarms and prepares to kill. Scully shoots him to prevent him from doing so, allowing Krycek to escape. Scully brings an unconscious Mulder to New Mexico. When Mulder awakens, Scully reveals that his behavior was caused by a drug placed in his water supply. She shot him because if he had killed Krycek, it would have been harder to prove his innocence in his father's death. She introduces him to Hosteen, who has been translating the files on the tape.

Scully reveals that the tape contains information on both her and Duane Barry. Hosteen introduces Mulder to his grandson, who drives him to the buried boxcar. Just before Mulder heads in, he is called by the Smoking Man, who is able to trace Mulder's location through the call. Mulder heads inside the boxcar and finds a pile of the dead creatures, each with smallpox vaccination scars on their arms. The Smoking Man arrives by helicopter with eight armed commandos and, not finding Mulder inside, orders the boxcar to be burned.