September, 1993 - "Pilot" FBI Special Agent Dana Scully is assigned to the X-Files Project, and told to debunk Special Agent Fox Mulder’s paranormal investigations. Mulder and Scully travel to Oregon to investigate several alleged-alien abductions. Their work and evidence are destroyed in a fire, but Scully retains a metal implant taken from one of the bodies.  She eventually gives the implant to Section Chief Blevins, her immediate supervisor, who gives it to the ominous Cigarette-Smoking Man.  He stores it in a special Pentagon storeroom. May, 1994 - "The Erlenmeyer Flask" Mulder is kidnaped by government agents. Mulder’s secret contact, Deep Throat, helps Scully infiltrate a secret installation and steal a cryogenically frozen alien fetus. When Deep Throat exchanges the fetus for Agent Mulder's release, Deep Throat is killed. The X-Files Project is closed down. October, 1994 - "Sleepless" Agent Alex Krycek is assigned to assist Agent Mulder in tracking down a psychic killer. ‘X’ replaces Deep Throat as Mulder’s government contact. October, 1994 - "Duane Barry," "Ascension" Duane Barry, an alleged alien abductee, kidnaps Scully. Mulder and Krycek pursue him to Skyland Mountain. Scully disappears.  Barry claims that she was taken by aliens. He dies after Mulder and then Krycek interrogate him. Mulder realizes that the Cigarette-Smoking Man is involved in Scully’s disappearance. Krycek kills several men, then disappears. Skinner re-opens the X-Files Project. November, 1994 - "One Breath" Scully’s unconscious body is found on the steps of a hospital. Her DNA shows signs of genetic tampering, and she is dying. Mulder breaks into the Cigarette-Smoking Man’s apartment and threatens to kill him. After considerable debate, Scully’s mother decides to disconnect Scully’s life support. Scully almost dies, but eventually recovers. February, 1995 - "Colony," "End Game" Agent Mulder discovers that his long-missing sister, Samantha, is still alive.  She begs him to destroy an Alien Bounty Hunter who is trying to kill her. Scully discovers that Samantha is one of a series of clones. Mulder tracks the Bounty Hunter to a submerged submarine in the Beaufort Sea. He attacks the Bounty Hunter, and contracts an alien retrovirus that nearly kills him. Scully saves his life. May, 1995 - "Anasazi," "Blessing Way," "Paper Clip" Mulder receives an encrypted computer disk containing the Defense Department’s top secret files on extraterrestrial life. Alex Krycek kills Mulder’s father to keep him from revealing government secrets. Mulder gives the encrypted disk to Albert Hosteen, who translates the encoded files. His nephew takes Mulder to a buried boxcar which contains ‘alien’ corpses. The Cigarette-Smoking Man orders his men to burn the boxcar. Mulder escapes, but nearly dies of exposure. Hosteen saves his life. Scully discovers a small computer chip embedded in her neck, and has it removed. At Mulder Sr’s funeral, the Well-Manicured Man warns Scully that her life is in danger. Alex Krycek goes to Scully’s apartment, planning to kill her, but shoots her sister Melissa by mistake. Hosteen gives Skinner the translated disk. Krycek attacks Skinner and steals the disk. The Well-Manicured Man tells Mulder and Scully about the alien spacecraft recovery in Roswell, in 1947. Skinner threatens to expose the Cigarette-Smoking Man if Mulder and Scully are hurt. Melissa dies. December, 1995 - "Nisei," "731" Scully learns that her implant collects information and artificially replicates mental processes. Mulder tracks several Japanese scientists, trying to learn more about their involvement in allegedly-alien autopsies. Scully believes that the ‘aliens’ are lepers who have been secretly irradiated. Mulder theorizes that the scientists have developed human-alien hybrids. ‘X’ rescues Mulder before he can be killed in a train explosion that destroys one of the strange creatures. February, 1996 - "Piper Maru," "Apocrypha" A salvage diver discovers the wreckage of a World War II fighter on the ocean floor--and is stunned to find a living pilot inside the plane.  The pilot's eyes are covered with a black membrane.  The diver returns to the surface. Now his eyes are totally black. Nearly everyone aboard the diver's ship, the Piper Maru, are killed by a mysterious radiation.  Mulder and Scully investigate the ship, and discover an oily film covering the diver’s suit. The diver returns home, and unknowingly transfers the black oil to his wife, who then travels to Hong Kong on business. Mulder follows her to Hong Kong, where he is attacked by Krycek. He subdues Krycek, and demands that the missing encrypted disk be returned. The diver’s wife follows Krycek into a bathroom, and transfers the black oil to him. Skinner is shot by Krycek’s accomplice, and nearly dies. Mulder and Krycek return to the U.S., to retrieve the translated digital tape. Another car crashes into them, and Krycek escapes. Mulder speculates that Krycek is the alien’s newest host. He contacts the Well-Manicured Man, who tells Mulder more about the sunken plane. Scully and Mulder track Krycek to a series of isolated silos, but the Cigarette-Smoking Man takes them into custody before they can discover a huge alien ship, and Krycek, locked deep inside one of the silos. The black oil leaves Krycek’s body, leaving him trapped in the silo. May, 1996 - "Talitha Cumi," "Herrenvolk" A ‘miracle worker,’ Jeremiah Smith, heals a mentally disturbed gunman and his victims. Mulder and Scully realize that he can change shapes, and that he has several identical clones. Mulder's mother meets with the Cigarette-Smoking Man at her summer home. They have an argument. After he leaves, she collapses, and is taken to a hospital by 'X,' who was secretly photographing the meeting. ‘X’ shows Mulder pictures of his mother with the Cigarette-Smoking Man. Mulder finds an alien gimlet stiletto hidden in the summer cottage. Scully takes Smith to meet with Mulder, but a Bounty Hunter intercepts them. They escape, and discover an eerie farm populated with teenage clones of Samantha and other children. The Bounty Hunter kills one of the Samantha clones, and the Smith clone. ‘X’ is killed in Mulder’s apartment, but leaves Mulder a clue about his murderers. Mulder meets Marita Covarrubias, who tells Mulder that the farm did not exist--but gives him a folder with pictures of the farm and the Samantha clones. The Cigarette-Smoking Man convinces the Bounty Hunter to heal Mulder’s mother. November, 1996 - "Tunguska," "Terma" Krycek contacts Mulder, and helps the agents intercept a Russian courier at the airport. The courier escapes, but they recover his diplomatic pouch, which carries a 4-billion-year-old extraterrestrial rock. A scientist drills into the rock, and black oil emerges to attack him. Marita Covarrubias helps Mulder travel to Tunguska, Siberia, where a massive fireball crashed to earth in Tunguska in 1908. Mulder takes Krycek along as a translator. They discover a prison camp at the crash site. The prisoners are mining the meteor for its black oil. Mulder and Krycek are captured and beaten. Krycek, who is in league with their captors, is released. Mulder is deliberately infected with the black oil, and given a crude antidote. He survives the experiment, and eventually escapes from the prison. Krycek is captured by a group of men who don't realize he's in league with the prison guards.  They cut off his left arm, as they've done with all the townspeople, to protect him from the black-oil experiments. January, 1997 - "Leonard Betts" Scully discovers that she has cancer. February, 1997 - "Memento Mori" Scully contacts other alleged-alien abductees. Most of them have died of cancer identical to hers. Skinner refuses to help Mulder meet with the Cigarette-Smoking Man, but secretly enlists his help to save Scully. Mulder and the Lone Gunmen encounter several clones in a medical facility. One of the clones shows Mulder tanks containing human forms, including Samantha’s, and a cold storage room containing vials of human ova. Scully’s name is on one of the vials. The eggs were harvested from women during their abductions, and later used for reproductions. Mulder doesn’t tell Scully about the vials. Despite her failing health, Scully elects to continue her work on the X-Files. November, 1997 - "Redux," "Redux II" Mulder infiltrates a secret research facility and discovers a vial which could contain a cure for Scully’s cancer. The Cigarette-Smoking Man tells Mulder that the vial holds a tiny microchip that will save Scully’s life. Scully collapses during an FBI panel investigation. When she regains consciousness, she agrees to have the microchip implanted in her neck. A Syndicate operative shoots the Cigarette-Smoking Man, presumably killing him. Scully’s cancer goes into miraculous remission. December, 1997 - "Christmas Carol," "Emily" Scully meets a little girl whose parents have been killed. Emily looks almost identical to herself as a child. She believes that Emily is actually her dead sister Melissa’s daughter, and tries to adopt her. DNA tests reveal that Scully herself is Emily’s true mother. Mulder reveals that Scully’s ova were removed during her abduction, and suggests that Emily was conceived from that stolen ova. A cyst on Emily’s neck suddenly oozes green, bubbling fluid which injures the physician treating her. Emily sickens after an Alien Bounty Hunter injects her with green fluid. She eventually dies. When Scully opens Emily’s casket, intending to autopsy her, she finds several small sandbags. Emily’s body is gone. March, 1998 - "Patient X," "The Red and The Black" ‘Faceless men’ begin killing large groups of abductees in Russia and America. Krycek exposes a Russian boy, Dmitri, to the black oil. Then he contacts the Syndicate, and offers to trade Dmitri for information about the black oil vaccine. Mulder and Scully meet Cassandra Spender, an alien abductee. Scully realizes that--like herself--Cassandra was abducted at Skyland Mountain, and has an implant in her neck.  She urges Cassandra not to remove the implant, for fear of contracting cancer. A large group of abductees meet at Skyland Mountain, where they are burned to death by the 'faceless men.'  Scully believes that their burning is somehow linked to her own abduction. Marita Covarrubias rescues Dmitri from Krycek, and tells Mulder about other mass burnings. The black-oil virus transfers from Dmitri to her. The Well-Manicured Man takes her to Ft. Marlene Air Force Base for treatment. Scully joins Cassandra and Dmitri at Ruskin Dam late at night. Suddenly they’re attacked by 'faceless men.' Most of the abductees are burned alive. Scully survives the attack, but can’t remember what happened. Cassandra disappears. The Well-Manicured Man captures Krycek, and offers him freedom in return for the Russian vaccine. He then injects Marita with the vaccine, hoping to save her life. May, 1998 - "The End" The Cigarette-Smoking Man is attacked in his forest hideout. He kills one man. The other, Alex Krycek, captures him and takes him to the Syndicate. Gibson Praise, a 12-year-old chess player, is nearly assassinated. Mulder realizes that Gibson is telepathic. His ex-partner, Diana Fowley, supports his theory. Fowley is assigned to guard Gibson. The Cigarette-Smoking Man shoots her, kidnaps Gibson, and turns the boy over to Krycek and the Well-Manicured Man for experimentation. Mulder accuses Jeffrey Spender, Cassandra’s son, of being in league with the Cigarette-Smoking Man. Spender denies his charges, and threatens to close down the X-Files. The Cigarette-Smoking Man steals Samantha’s file from Mulder’s office. Then he sets fire to the office. He tells Jeffrey that he’s really his father, then escapes in the confusion when smoke alarms begin ringing. July, 1998 - "Fight The Future" Mulder and Scully are assigned to investigate an alleged-terrorist threat to a Dallas government building.  They find a bomb in an adjacent building, and manage to evaluate the building before the bomb explodes.  Although they saved thousands of lives, they receive formal reprimands for not following orders and maintaining surveillance on the original building.  Scully becomes discouraged, and decides to leave the FBI. Mulder talks Scully into investigating more reports of the black oil virus in Texas. Scully is infected with the virus.  Mysterious paramedics rush her to Antarctica in cryogenic storage. The Well-Manicured Man gives Mulder coordinates to find Scully, and a vial of antidote. Then his car blows up, presumably killing him. Mulder travels to Antarctica, where he discovers thousands of humans frozen in cryogenic storage tanks.  Most of them have aliens growing inside them.  He finds Scully and injects her with the antidote. The aliens begin to awaken, and chase him through the ship. He and Scully barely escape. The ship takes off, leaving Mulder and Scully stranded in the snow. Scully realizes that since the antidote worked, a cure against the 'black-oil virus' can eventually be found.  She decides to continue her work on the X-Files. November, 1998 - "The Beginning" Mulder and Scully investigate a bizarre death in Arizona. Mulder theorizes that the victim was infected by the alien virus, and an alien erupted from inside his body, killing him. The Cigarette-Smoking Man’s medical team has been operating on Gibson’s brain, trying to learn why he has psychic abilities.  He believes that Gibson will be able to communicate with the alien creature, and brings Gibson to Arizona to find it. Mulder and Scully investigate a nearby power plant, where another man has been murdered. Gibson hides in their car. Scully takes him to a hospital for treatment. She discovers that Gibson has traces of the alien virus in his body. While she’s calling Mulder, a Syndicate operative kidnaps the boy and takes him back to the power plant. Diana Fowley takes Mulder into the power plant, where they search for the alien. The alien kills the Syndicate operative. FBI agents apprehend Mulder before he can rescue Gibson, who vanishes. Mulder and Scully are put on probation, and assigned to Assistant Director Kersh. February, 1999 - "Two Fathers," "One Son" Cassandra Spender is found in a Virginia stockyard, unharmed. The surgeons operating on her have been burned alive. She warns Mulder and Scully that the aliens plan to conquer the universe by infecting all life forms with the black oil virus. Mulder and Scully learn that the Cigarette-Smoking Man, also known as "C.G.B. Spender," may have some connection to Cassandra, Jeffrey, and Mulder's missing sister Samantha, since Cassandra was originally abducted the same night as Mulder’s sister--November 27, 1973. Cassandra rushes to Mulder’s apartment, and begs him to kill her. She claims to be the first successful human/alien hybrid. She believes that the aliens won’t begin their Colonization Project if they don’t know the hybrid experiments were successful. CDC agents break into the apartment. Mulder, Scully, and Cassandra are quarantined at the Ft. Marlene military base. Mulder learns that the Syndicate has been experimenting on Marita Covarrubias, trying to find a viable antidote against the black oil virus. The Syndicate members meet at El Rico Air Force Base to turn over Cassandra to the aliens. Faceless rebels break in, and kill them all. Diana Fowley and the Cigarette-Smoking Man barely escape. Jeffrey Spender takes responsibility for the Syndicate deaths, and recommends to A.D. Kersh that Mulder and Scully be reinstated on the X-Files. The Cigarette-Smoking Man shoots Jeffrey, presumably killing him. May, 1999 - "Biogenesis," "The Sixth Extinction," "Amor Fati" While Mulder and Scully investigate the death of an African scientist, Mulder hears an unexplained riot of sound in his head each time he’s exposed to a carbon rubbing of an allegedly-alien artifact. These attacks give him a precognitive awareness. He collapses on a stairwell. Diana Fowley informs the Cigarette-Smoking Man that Mulder is suffering from psychic attacks, and hospitalizes him in a psychiatric ward. Scully travels to Africa to learn more about the artifacts, and discovers a massive craft buried in the sand where the artifacts were discovered. She studies the alien symbols covering the craft, and realizes that they describe human genetics and quote ancient religious passages.  Strange things happen to the local tribesmen. Mulder becomes violent, but manages to enlist Skinner’s aid. Skinner contacts Kritschgau, who explains that Mulder is experiencing ESP episodes. The electrical impulses in his brain are working harder than his body can sustain. They subject Mulder to a series of tests that prove he’s developed heightened psychic abilities. Skinner and Kritschgau try to help Mulder escape from the hospital, but Diana Fowley intervenes. Mulder suffers severe convulsions, then becomes comatose. When Scully returns home, Kritschgau tells her that Mulder became ill because radiation from the rubbing activated the alien virus he received in Tunguska two years previously. Mulder’s mother checks him out of the hospital. Scully learns that the Cigarette-Smoking Man was involved. Mulder experiences idyllic visions of a new life, and meets his old ally, Deep Throat, who apparently lives nearby. Diana Fowley joins Mulder, and they spend the night together. Then she takes him to the Cigarette-Smoking Man’s house, where his sister Samantha lives. Scully receives a book about Native American practices, and learns about a myth foretelling a mass extinction. She deduces that the Cigarette-Smoking Man thinks Mulder’s illness is protection against a coming plague. Kritschgau believes that Mulder has biologically transformed into an alien. While Mulder dreams of living a full and happy life with Diana Fowley, and the world’s destruction by aliens, in reality he is being operated on by scientists who transplant his alien genetic material into the Cigarette-Smoking Man's brain. Scully is given a key card that leads her to the surgical facility where Mulder is being held. She rescues him, and brings him home. Diana Fowley is murdered. Scully realizes that Diana gave her the myth book and key card, to help save Mulder from the Cigarette-Smoking Man. February, 2000 - "Sein Und Zeit," "Closure" A little girl’s mysterious disappearance reminds Mulder of his sister’s kidnaping. He receives a troubled call from his mother, who later commits suicide.  When Scully autopsies Mrs. Mulder, she finds that the older woman was dying of cancer, and chose to end her life in her own way. Mulder is told that his sister is with the ‘walk-ins’--old souls wandering in the starlight who protect other souls from harm that they would have suffered in real life. Mulder and Scully discover dozens of graves at a Santa’s Village. They arrest the ‘Santa,’ and excavate many small bodies from the graves. Psychic Harold Piller helps Mulder find clues about Samantha’s disappearance. They travel to April Air Force Base, where they find proof that she lived there after her abduction. Mulder believes that she was given to the Cigarette-Smoking Man, and raised with Jeffrey Spender, while more tests were conducted on her. Mulder finds Samantha’s diary, which tells how the tests have taken away most of her memories. Scully uncovers a 1979 police report about a runaway who matched Samantha’s description. Scully meets with the emergency room nurse who treated Samantha. The nurse tells her she had a vision that Samantha was murdered. But when the Cigarette-Smoking Man came to collect Samantha, she had vanished. Mulder is led into a starlit field by a small ghostly child, where he sees Samantha’s ghost. They reunite, and Mulder finally finds inner peace. March, 2000 - "En Ami" Scully investigates the ‘miraculous cure’ of a young boy suffering from terminal cancer. The Cigarette-Smoking Man claims responsibility for his cure, and entices Scully into traveling with him to visit other people he’s cured. He tells her he’s dying of cerebral inflammation caused by recent brain surgery, and wants to give her the ultimate cure for cancer. Mulder discovers messages on Scully’s computer from an operative at the Department of Defense called ‘Cobra.’  He believes someone hacked into her computer to establish contact with Cobra. The Cigarette-Smoking Man takes Scully to dinner at a fancy restaurant, where they are supposed to meet Cobra. The Cigarette-Smoking Man admits that Cobra’s research is a cure for all human diseases, not just cancer. Cobra doesn’t show up, but Scully finds a note under her plate instructing her to meet him the next morning. Cobra meets Scully in the middle of the lake, and gives her his research disk. Before he can explain what’s on the disk, an assassin shoots him from the shore. The Cigarette-Smoking Man kills the assassin before Scully can be harmed. Scully furiously gives the disk to the Cigarette-Smoking Man, but he hands it back to her, and she returns home. Later she finds that he switched disks with her. The Cigarette-Smoking Man destroys the real disk by throwing it into the lake. May, 2000 - "Requiem" Mulder and Scully return to Oregon, the site of their first case together, to investigate more alleged alien abductions. Marita Covarrubias releases Krycek from a Tunisian prison, and brings him to the ailing Cigarette-Smoking Man. He tells them that an alien ship collided with a military aircraft in Oregon, and he needs them to recover it so they can rebuild the Alien Colonization Project. Scully experiences vertigo attacks while they investigate several peoples’ mysterious disappearances. When Mulder and Scully return home, Skinner shocks them by bringing Krycek and Marita Covarrubias to their office. Mulder tries to attack Krycek, but Skinner protects him. Krycek tells them that the Cigarette-Smoking Man’s final wish is to rebuild the Project, and he will do anything to prevent that. He tells Mulder where to find the missing spacecraft. Mulder believes that previous abductees are being collected, and won’t allow Scully to return to Oregon. She remains in Washington with the Lone Gunmen, studying the abductees’ medical reports, while Skinner accompanies Mulder to Oregon. Too late, she realizes that Mulder is actually the one in danger. But before she can warn him, she collapses. Mulder and Skinner set up a perimeter of laser beams to find the missing ship. When Mulder steps through the ship’s force field, he finds the missing abductees inside.  He is unable to free them, or escape himself. Skinner realizes that Mulder is missing. A moment later, he sees a spaceship appear overhead and fly away. Skinner returns to Washington, and tells Scully that Mulder has disappeared. She promises that they’ll find him, and confides to Skinner that somehow, despite being barren for several years, she’s pregnant. May, 2000 - "Within," "Without" Deputy Director Kersh has taken charge of the manhunt to find Mulder. The task force leader, Agent John Doggett, tries to shake Scully’s faith in her partner, but is unsuccessful. Doggett discovers that Mulder was dying from continued abnormal brain activity. He believes that Mulder staged his own disappearance, so that his work on the X-Files wouldn’t appear to be a failure. The Lone Gunmen track the spaceship’s course to Arizona. Scully realizes that the Bounty Hunter’s next victim will be Gibson Praise, who is hiding at a deaf school in Arizona. She and Skinner rush to find the boy. Doggett receives a similar lead, and their paths cross at the school. ‘Mulder’ grabs Gibson and drags him from the school. Doggett follows them, and threatens to shoot him. Gibson breaks away from him, and ‘Mulder’ deliberately steps off the cliff. Scully realizes that ‘Mulder’ is actually the Bounty Hunter. Gibson has escaped, and she follows his best friend to an underground cavern in the desert where he’s hiding. Then she returns to Skinner at the deaf school, where the Bounty Hunter has been morphing into different people--including her--to hide. Skinner takes Gibson to the hospital to treat his broken ankle, while Scully wanders in the desert, searching for the alien ship. Doggett finds her there, unknowingly only feet away from the craft’s force field, and she heads to the hospital with him. The Bounty Hunter attacks Skinner and snatches Gibson, then morphs into Skinner and attacks Scully. She shoots and kills him.  Skinner's face is burned, but he survives. Doggett tells Scully he’s been assigned to the X-Files, and promises to find Mulder. July, 2000 - "Per Manum" Scully flashbacks to several conversations with Mulder regarding her inability to have children, and her failed attempt to conceive in vitro with the stolen ova Mulder found four years previously. When she’s warned by another pregnant woman that both their infants may be at risk, she asks for a leave of absence. The two women go to the Walden-Freedman Research Center for a second opinion about whether their babies are human and healthy. Doggett contacts Knowle Rohrer, an old friend, for information. Scully realizes that they are still in danger, and the two women escape. Knowle appears, claiming that Doggett sent him, and drives the women away. Scully’s friend goes into labor. Knowle drugs Scully so she can’t witness the birth, but she hears the cry of an alien baby. Doggett visits her at the hospital, and assures her that the baby was normal. He asks why she didn’t reveal her own pregnancy, and she admits that she was afraid she’d be taken off the X-Files. He promises again to help her find Mulder. August, 2000 - "This Is Not Happening" Teresa Hoese, who was kidnaped in Oregon a few months ago, is found in a remote Montana field. She has been tortured, and is horribly scarred. Skinner and Doggett tell Scully about Teresa’s return, and they travel to Montana to visit her. The ‘miracle worker,’ Jeremiah Smith, morphs into Teresa’s doctor, and arranges for her to be transferred from the hospital. He places his hand on her face, and heals all her scars. Doggett brings Special Agent Monica Reyes into the case, because of her experience with cult abuse cases. Reyes later sees another spaceship land, and drop off two bodies. She stops Jeremiah Smith and Absalom, the leader of a nearby doomsday cult, from taking one of the bodies--another missing Oregon abductee. The agents accompany a SWAT team to round up the cult. Teresa is there, but can’t explain what happened to her. Scully realizes that Jeremiah Smith is healing the abductees. She confronts him, and he begs her for protection from the aliens. Doggett finds Mulder’s lifeless body outside the compound. Scully rushes back to the compound so Jeremiah can heal him--but an alien spaceship appears, and takes him away. Skinner, Scully, Doggett, Kersh, and the Lone Gunmen attend Mulder’s funeral. November, 2000 - "DeadAlive" Billy Miles’ drowned body is found in the ocean. During a routine autopsy, he exhibits sudden signs of life. Skinner realizes that if Miles is still alive, Mulder might be, too. He and Doggett unearth Mulder, who is clinically alive but in a state of decomposition. Billy Miles wakes up, and showers off a thick layer of bloated skin. Perfectly healthy, he walks into the corridor and disappears. Krycek appears and tells Skinner he has an antidote that will save Mulder’s life--but Skinner must convince Scully to sacrifice her unborn baby. Doggett attacks Krycek, who deliberately drops and shatters the antidote vial. Scully operates on Mulder, and realizes that life support was incubating the alien virus. She devises an ingenious series of anti-virals to destroy the virus.  He regains consciousness soon afterwards. Scully tells him that his brain disorder is completely cured. His facial scars eventually heal. January, 2001 - "Essence," "Existence" Scully is about to have her baby.  Billy Miles returns and begins stalking her.  Krycek suddenly appears and offers to save her from Miles, in exchange for Mulder's life.  Monica Reyes takes Scully to a secret place known only to Doggett and her, where she can hide in safety until the baby's birth. Skinner, Mulder, and Doggett kill Billy Miles by pitching him over the edge of a building, and into a trash compactor.  His body is crushed. Krycek confronts the three agents in the FBI's garage.  He tries to convince Skinner to kill Mulder.  Skinner shoots Krycek between the eyes.  Doggett tells Mulder where to find Scully and Reyes, and Mulder leaves. Billy Miles' body is recovered from the compactor, and taken to the morgue.  The medic in charge notices an odd piece of metal that looks like a section of spinal vertebrae mixed in with Miles' crushed bones. When he leaves the room, the metal piece begins to spin around, and multiply.  A few minutes later, Billy Miles stands up and walks out of the room.  He appears to be uninjured. Scully and Reyes take refuge in the abandoned town where Doggett was born.  While they're cleaning one of the buildings in preparation for the baby's birth, they realize that someone is stalking them.  Monica shoots the man, and identifies him as Billy Miles. Scully goes into labor.  As her baby is being born, Billy Miles' injuries vanish, and he stands up again.  Other supersoldiers join him, and watch the baby's birth from the doorway.  Despite Scully's concerns over whether her baby is human or an alien hybrid, it appears perfectly normal. Surprisingly, the watching supersoldiers don’t harm Scully or her baby.  After the birth, they quietly disperse.  Mulder arrives by helicopter just in time to see them leaving. Scully names the baby William, after Mulder’s dead father. She and Mulder admit that they really do love each other. Mulder accepts William as his son. A few days later, Mulder disappears. Scully tells Doggett that he’s gone into hiding. Doggett tells her that Krycek's body has vanished, and that the security tapes of his death were all changed to hide the event. She urges Doggett to abandon his investigation against Kersh. Doggett asks Monica Reyes to officially join him on the X-Files Project. The hanging mobile above William’s bassinet suddenly begins moving on its own. Scully is frightened by her son’s telekinetic abilities, and begs Doggett to continue his investigation. February, 2001 - "Nothing Important Happened Today - II" Scully and Doggett investigate a merchant marine vessel where several people have died. They find a hidden lab where scientists were manipulating human ova for transplantation. Scully desperately tries to discover if William’s records are in the lab. Doggett pulls her out just before the ship explodes. April, 2001 - "Trust No 1" Scully gives into pressure from Doggett’s mysterious source who claims he has information about the alien supersoldiers, and contacts Mulder. Too late, she realizes that Doggett’s source is a supersoldier himself, and plans to kill Mulder. When Mulder jumps off the train near a rock quarry, she and Doggett try to find him. The supersoldier tries to kill her, but is destroyed when he comes too close to a wall of magnetite, a rare magnetic ore. May, 2001 - "Provenance," "Providence" When more pieces from an alien spacecraft are recovered in Canada, Scully realizes that a UFO cult wants to kidnap William. She gives the baby to the Lone Gunmen for protection, but they’re attacked, and William is taken. They track the kidnapers to Pennsylvania. The cult leader offers to return William to Scully in return for confirmation of Mulder’s death. The baby’s crying activates the half-buried spaceship, which incinerates the cult members as it takes off--but leaves William completely unharmed. Scully recovers her baby, and takes him home again. July, 2001 - "Jump The Shark" The Lone Gunmen are killed when they try to stop a bio-terrorist from murdering millions of innocent people. July, 2001 - "William" Doggett is attacked by a deformed man who breaks into his office. When the man is captured, he tells Scully that he’s searching for information about the alien conspiracy. He claims that he was injected with something that burned and disfigured him. Doggett theorizes that the deformed man is Mulder. Scully insists that he’s wrong, but DNA tests indicate that Doggett may be right. The deformed man injects William with magnetite, which elevates his blood’s iron count, and removes his special telekinetic powers. Scully realizes that the deformed man is Jeffrey Spender, Mulder’s half-brother. Jeffrey tells her that his disfiguration is the result of the Cigarette-Smoking Man's genetic experiments.  He warns her that the alien supersoldiers will always stalk William, even though he no longer has any special powers. Scully vows to protect her baby--but knows that she can’t. She makes the painful decision to give him up for adoption, so that he can grow up happy and safe in total anonymity. January, 2002 - "The Truth" Mulder infiltrates a secret government installation, and is caught by Knowle Rohrer. They struggle until Knowle falls over a railing, and is electrocuted in some high-voltage wires. Mulder is captured, and thrown in jail. His captors torture him daily until they believe he’s been brainwashed into admitting his own guilt. Kersh informs Skinner and Scully that Mulder is being held in prison. They visit him, but he insists that he’s guilty and deserves punishment. Bewildered, they leave. Mulder sees an image of Alex Krycek, who insists that Mulder needs his help to escape. Kersh is told to hold an FBI trial that will convict Mulder of murdering Knowle Rohrer. Scully and Skinner visit Mulder again. This time, knowing he’s not being watched, he behaves normally. Doggett and Reyes join them, and promise to help him. Mulder asks Skinner to defend him in the upcoming trial. He confides to Scully that he learned something terrible at the secret facility, but won’t divulge what he learned. Mulder’s trial is a mockery. Skinner’s witnesses--his agents--testify about Mulder’s past experiences, his history with the Bureau, and vigorously proclaim his innocence, but neither Kersh nor the other ‘judges’ take them seriously. Skinner also questions Jeffrey Spender, to no avail. Mulder sees an image of ‘X,’ who gives him Marita Covarrubias’ address. Skinner contacts her, and persuades her to testify on Mulder’s behalf. Gibson Praise emerges from hiding, and insists on testifying to protect Mulder. Gibson reveals his telepathic abilities to the judges, and identifies one of them as an alien supersoldier. The prosecuting attorney claims that Knowle Rohrer’s body was recovered and identified. Scully manages to examine the body, and realizes that it’s not Knowle. She tries to present evidence at the trial, but is ignored. Mulder is sentences to death by lethal injection. Skinner and his agents break him out of jail before Knowle can kill him. Kersh helps them escape, and tells Mulder to head for Canada. Mulder disobeys him, and takes Scully south to the Anasazi ruins in New Mexico. There they find the Cigarette-Smoking Man hiding amid the ruins. He’s nearly dead, but he tells them that the aliens will carry out their final attack on December 22, 2012. Doggett and Reyes follow Mulder and Scully to the ruins, where they are attacked by supersoldier Knowle Rohrer. They shoot at him, but he’s unharmed by their bullets. He pursues them toward the ruins, not realizing that they have a high magnetite content. When he gets too close, he’s sucked into the cliff and destroyed. Two black helicopters close in on the ruins, and blast it into powder. Mulder and Scully barely escape. The Cigarette-Smoking Man is finally, definitively killed. Mulder and Scully take refuge in a nearby hotel. Mulder insists that he failed to prevent the alien takeover, but Scully reassures him that they still have a chance to win. She finally persuades him that there’s still hope for the future.