Fox Mulder's work on the X-files (1994-1998)

was reassigned to the X-Files in 1994, following a short interval in which the cases were closed. ( "Ascension") Mulder continued to investigate the X-files with usual partner, , over the next four years. ( "Firewalker" - "The End")
==History==
===1994===
The X-Files were re-opened by Assistant Director Skinner, who realized that the Cigarette-Smoking Man and those working for him were most afraid of that happening. ( "Ascension") Mulder later recalled that he had "worked [his] ass off to get the files reopened". ( "Never Again") With the loss of both Krycek and Scully, Mulder returned to his office alone. He removed dusty plastic wrapping that covered every piece of furniture in his office, including his desk and the cabinet containing the X-Files. Scully's disappearance had recently been added to the files with the case number 73317.
:It is unknown when this X-File was added to the other files but it is slightly puzzling that it was already in the cabinet containing the files before the plastic wrapping had been removed from Mulder's office as the X-Files, and presumably the office, had been closed prior to Scully's disappearance.
In Los Angeles, California, Mulder investigated the Trinity Killers, who believed themselves to be vampires, and a woman named Kristen Kilar. She and the Trinity Killers had murdered more than seven people in three states of the US. Mulder added the case to the X-Files, with the case number X256933VW, but became romantically involved with Kilar while investigating the case. The four murderers ultimately burned to death in a fire caused by Kilar. ( "3")
Shortly thereafter, Mulder learned that Scully had been admitted to Washington, D.C.'s Northeast Georgetown Medical Center in critical condition. He traveled to the hospital with her mother and demanded to know how Scully had arrived there, but he was provided with no answers. Mulder consulted the Lone Gunmen, who, with the help of their latest member, a hacker known as "the Thinker", diagnosed Scully's condition. Nevertheless, frustrated at the lack of evidence, Mulder handed in his resignation but it was seen as unacceptable and was therefore refused. ( "") After Scully recovered, Mulder decided to continue working on the X-Files with her. ( "", "Firewalker")
One of the first cases they investigated upon their return to the X-Files led them to the man who had killed Deep Throat. The man was shot and killed during the investigation, which was added to the X-Files with the case number XWC060361. ( "Red Museum")
Mulder soon learned that Andy Schneider, a member of the Mutual UFO Network who he personally did not know, was familiar with him. Andy Schneider had given Mulder's details to FBI Agent Moe Bocks, who required Mulder's help on a case that involved the discovery of a mutilated body found in an unearthed grave. Agent Bocks was unaware that Mulder had previously encountered unearthed graves while working in the FBI's Violent Crimes Section. While Mulder worked on the case with Agents Bocks and Scully, he admitted he had previously seen similarly horrific cases break agents with twenty years' field experience. He was later instrumental in finding the criminal, named , who was ultimately jailed. ( "Irresistible")
===1995===
In early 1995, Mulder learned that identical clones were being systematically killed by a shape-shifting Alien Bounty Hunter, which at one point assumed Mulder's appearance in a failed attempt to fool Scully. ( "Colony", "End Game") In pursuit of the bounty hunter, Mulder journeyed to the Arctic alone but was unable to stop the alien from leaving. Mulder suffered simultaneously from exposure to extreme cold and the bounty hunter's "blood", which acted as a deadly alien virus. A naval reconnaissance squad found Mulder and took him to Eisenhower Field. After Scully, who had studied the virus, located him there, she saved him by demanding that his body be placed in a cold environment and he gradually then recovered. ( "End Game")
On a mission in the North Atlantic Ocean with Scully, Mulder and his partner experienced accelerated aging. Unlike Scully, Mulder's aging was not slowed by the consumption of water and he ultimately lost consciousness, though he and Scully were eventually rescued and received medical care. ( "Død Kalm")
Later that year, Mulder helped a group of Romanian elders perform a successful exorcism that separated Charlie Holvey's soul from a dark and malevolent force said to have previously existed as Cain, Lucifer and Hitler. During the ceremony, Mulder was told that if he looked at the possessed Charlie, the evil spirit would recognize him, but he did not heed the advice. After the exorcism, Mulder was advised to be careful as the dangerous force now knew him. ( "The Căluşari")
In April 1995, Mulder learned that "the Thinker" had hacked into the Department of Defense computer system and stolen classified MJ documents, containing details on every encounter with UFOs since the Roswell incident. The files were given to Mulder when he met with "the Thinker", who was murdered, execution style, shortly thereafter.
At night, Mulder's father was shot to death in his house by an unknown assassin while Mulder was in another room of the house. In the same month, Mulder's life was threatened several times, both by the Cigarette-Smoking Man - who desperately wanted the MJ documents - and Alex Krycek - who stopped working for the Cigarette-Smoking Man around the same time. Believing that Krycek may have killed Mulder's father, Scully shot her partner in order to save him from shooting Krycek. Mulder recovered in Los Alamos, New Mexico, but the Cigarette-Smoking Man later managed to trap him in a locked boxcar there and he almost died. He was recovered and miraculously nursed back to health by local Navajo healer, Albert Hosteen.
After his recovery, Mulder learned that, around 1973, his father had secretly been working with the Cigarette-Smoking Man, Deep Throat and others, on a scientific project that had originated in Nazi Germany. When Mulder and Scully traveled to the Strughold Mining Company, where the project had been based, they found a tunnel in which many medical files were stored, including documents on Scully and Mulder's sister - a file that had originally been Mulder's. Another man who had secretly been working there, the , explained to Mulder that he and his colleagues had been attempting to create a human-alien hybrid.
Although the MJ documents were ultimately destroyed, Skinner traded the continued secrecy of the information within the classified files for Mulder and Scully's safety. Mulder was unaware that the MJ documents had been destroyed but the death of his father motivated him to return to the X-Files with a renewed sense of determination. ( "Anasazi", "The Blessing Way", "Paper Clip")
:Mulder seems shocked to learn of his father's part in the conspiracy. This seems slightly puzzling as "Travelers" establishes that Mulder was told about his father's involvement by former FBI Agent Arthur Dales in 1989.
Months later, Mulder learned that a group of Japanese scientists had also been continuing the attempts started by Nazis to create a human/alien hybrid, but were being systematically murdered. ( "Nisei") He again became locked in a boxcar, this time with one of the men responsible for murdering the Japanese scientists. The boxcar was rigged to a bomb and was adjacent to another locked car containing a deformed humanoid that seemed alien. Ultimately, Mulder was unconsciously rescued from the boxcar by X, who also killed the man who had murdered the Japanese scientists, but the deformed humanoid died when the car exploded. ( "731")
During this investigation, Mulder found evidence which suggested that an American salvage ship, the Talapus, had retrieved a UFO from the bottom of the Pacific Ocean and had secretly transported the craft and its occupant to Newport News, Virginia. As usual, Scully's opinion differed from Mulder's and she believed that the "UFO" was actually a Russian submarine. ( "Nisei")
===1996===
In early 1996, Agent William Patterson - Mulder's former instructor from the Investigative Support Unit - requested that Skinner assign Mulder to an unexplained murder case that Patterson and the ISU were already assigned to. Skinner did so, but the fact that Agent Patterson had requested him was initially unknown to Mulder. During the investigation, Mulder attempted to follow Patterson's past advice of studying an artist's art in order to know the artist and struggled to understand the killer. At first, he was suspected of involvement in the murders but eventually realized that Agent Patterson was the actual killer. Mulder shot Patterson, but he survived and was later jailed. ( "Grotesque")
Mulder discovered that a French salvage ship, the Piper Maru, had journeyed to the same location where the Talapus had retrieved a craft from the bottom of the Pacific Ocean. The Piper Maru's crew had been exposed to extremely high levels of radiation, but the source of the contaminant was undetermined. During the investigation, Mulder located Alex Krycek in Hong Kong, who offered to lead him to the MJ documents in Washington, D.C.. Unknown to Mulder, however, Krycek was soon possessed by an oil-like substance that Scully and Mulder would come to know as "". ( "Piper Maru")
While driving through Maryland at night, Krycek and Mulder were forced off the road by two men. Mulder saw a bright flash as the black oil within Krycek irradiated the men and he soon lost consciousness. Once again losing track of Krycek, Mulder was hospitalized in Northeast Georgetown Medical Center. Once released, he determined that Krycek had been possessed by the black oil, which had also irradiated the Piper Maru's crew. The search for the possessed Krycek led Mulder and Scully to an abandoned missile silo in Black Crow, North Dakota, where Mulder correctly suspected the UFO that had been retrieved from the bottom of the Pacific Ocean was stored. The agents found bodies of men with radiation burns inside the facility, but were forced off the premises by soldiers working for the Cigarette-Smoking Man before they could locate Krycek. ( "Apocrypha")
With Scully, Mulder investigated - a highly intelligent but extremely dangerous serial killer. Modell was searching for a "worthy adversary" and, believing that Mulder might fit the role, the killer taunted him throughout the investigation. ( "Pusher") In a downtown hospital, Modell brandished a firearm and tried to motivate Mulder to shoot Scully in retaliation for her shooting him earlier. ( "Pusher", "Anasazi") Although Modell had caused the deaths of another FBI agent and a Loudon County Sheriff's deputy, Mulder managed to resist Modell and shot the criminal. The agents apprehended the killer, who was ultimately convicted on charges stemming from the incident in the hospital. When Mulder and Scully last saw him, Modell was comatose with Mulder's bullet in his head. His last prime target had been Mulder. ( "Pusher")
With Scully, Mulder investigated Assistant Director Skinner's involvement in the murder of prostitute Carina Sayles. Though Skinner was dismissed from the FBI, Mulder eventually proved that Skinner was innocent and that a conspiracy of men had been trying to weaken Scully and himself by removing Skinner, who had been protecting the agents. Mulder was unaware that the men were working for the Cigarette-Smoking Man. ( "Avatar")
While investigating several murders committed by otherwise ordinary citizens, Mulder and Scully were both exposed to an altered television signal. The fact that Mulder was red-green colorblind made him immune to the altered signal, however. He later learned that the signal had been part of a mind-control experiment conducted under the supervision of the Cigarette-Smoking Man. ( "Wetwired")
Shortly thereafter, Mulder encountered Jeremiah Smith, a man with amazing healing abilities. Mulder helped Jeremiah Smith to escape from an alien bounty hunter in the hope that Smith would heal his injured mother, who had just suffered a stroke. ( "Talitha Cumi") However, Smith took Mulder to Canada where he saw several male and female clones working on a farm near a cave containing many bees. ( "Herrenvolk") Around this time, Mulder consulted a doctor named Peter Valedespino regarding killer bees. ( "Zero Sum") Additionally, X was killed for providing Mulder with information, although he left a message in blood as he died. The message, "SRSG", led Mulder to the Special Representative to the Secretary General of the United Nations, where he met . She informed him that an investigation into the Canadian farmland had proven unsuccessful. ( "Herrenvolk") However, Mulder would continue to approach her for information on several subsequent occasions in 1996. ( "Herrenvolk", "Teliko", "Tunguska", "Unrequited")
While working on a case involving the disappearances of four men in Philadelphia, one of whom had been found dead with a seed from a rare plant in his body, Mulder was injured by a similar seed and became temporarily paralyzed as a result. ( "Teliko")
During an investigation into the Temple of the Seven Stars cult and its leader, Vernon Ephesian, Mulder and Scully discovered evidence that suggested Mulder had been reincarnated at least twice, having previously lived as a soldier during the American Civil War and as a Jewish woman in Poland during World War II. ( "The Field Where I Died")
Soon after, Mulder was provided with evidence suggesting that the Cigarette-Smoking Man had been keeping an interest in his work on the X-Files since before December 24, 1991, and that Scully's assignment to the files had originally been secretly arranged and supervised by the Cigarette-Smoking Man. ( "")
While investigating a black rock which may have come from Mars and seemingly contained black oil, Mulder was taken prisoner in Tunguska, Russia. Trapped in a Russian gulag where the prisoners mined the rock for what seemed to be black oil, Mulder was injected with an unknown substance and he, along with many other prisoners, was infected with a form of the black oil as part of an experiment. ( "Tunkuska") After he regained consciousness in his cell, a prisoner in the cell adjacent to his told him that he had actually been infected with the , which the prisoners mined in the Tunguska rock. The substance that Mulder had been injected with earlier was actually a cure for the black cancer. Mulder later escaped from the gulag and was found by a Russian family who helped him travel to St. Petersburg, from where he returned to the US. Upon his return, he narrowly avoided an explosion in North Dakota that destroyed much of the alien black oil in the country. ( "Terma")
Shortly thereafter, a recurring dream that Mulder had been experiencing lead him to recover the body of John Lee Roche's fourteenth victim. Scully believed that Mulder may have been unconsciously thinking about the case since he first investigated the killer and reminded Mulder that he had once stated, "a dream is an answer to a question we haven't learned how to ask". With the continued help of Mulder's dreams, he and Scully located evidence that Roche had killed sixteen girls. After the body of the fifteenth victim was found, Mulder became unintentionally responsible for Roche's escape. The criminal kidnapped another girl, who was freed when Mulder shot and killed Roche. ( "Paper Hearts")
:Scully's recollection that Mulder once said, "a dream is an answer to a question we haven't learned how to ask" is a paraphrased version of a statement he makes in "Aubrey", in which he says, "I've often felt that dreams are answers to questions we haven't yet figured out how to ask".
===1997===
In early 1997, Mulder was forced to adhere to FBI regulations and take his first vacation in four years. Before he left, he asked Scully to continue investigating a case she had unenthusiastically been working on with Mulder. The case involved claims of two alien craft which had reportedly crashed and been retrieved from the Sea of Barents, before employees at a military space center in the Republic of Karelia had been assigned to work on them. While Scully journeyed to Philadelphia in order to investigate the claims, Mulder made a "spiritual" journey to Memphis, Tennessee, where Elvis Presley had lived. Believing the claims of alien craft to be bogus, Scully handed the case over to the Bureau field office in Philadelphia. Mulder was appalled when he learned this during a phone call to Scully, but he later also came to the conclusion that the claims had been fictitious. He returned from Memphis a week after he had traveled there. Once Scully returned, Mulder decided that they should investigate reports of the image of a missing child that was appearing on a blank billboard outside of Arlington. ( "Never Again")
:It is unclear whether Mulder and Scully concluded the investigation pertaining to the billboard near Arlington, as Mulder only begins the case in the final scene of "Never Again".
Shortly thereafter, Scully informed Mulder that she had cancer. ( "Memento Mori") The previous year, Scully had met a group of women, purported abductees, who had developed cancer after having had implants removed from the base of their necks. ( "Nisei") Although all but one woman had died as a result of their cancer, Mulder tried to determine what else he could learn about the group while Scully was hospitalized.
He came to realize that Scully's cancer was also most probably a result of her abduction and that some of the women had been undergoing treatment for infertility at a federally-operated specialized clinic. After he broke into the clinic, he discovered a file - a directory for a mainframe in the Lombard Research Facility - that contained Scully's name. Mulder subsequently broke into the Lombard Research Facility and was shocked to discover a group of clones inside the facility who were attempting to develop more clones in their own image, using human ova extracted from the group of female abductees. The ova included those belonging to Scully, which had been harvested during her abduction. An armed man shot at Mulder before he managed to safely escape the facility. Although Mulder had taken Scully's ova with him, he did not inform her of his discovery. They watched in the hospital where she was undergoing treatment as the surviving member of the group of female abductees peacefully died. Believing that she had to learn to live with cancer, Scully returned to work on the X-Files with Mulder. ( "Memento Mori")
During their next case, a neo-Nazi copy shop owner suspected Mulder of working with Jews and commented that he at least looked like a Jew. Mulder did not respond to the remark, however, and simply laughed. While investigating the same case, Mulder was later attacked by a golem but survived the assault relatively uninjured. ( "Kaddish")
:For an essay discussing the possibility that Mulder was Jewish, click here.
On February 23, 1997, a woman came to Mulder and Scully in a Washington, D.C. bar and told them that her brother, Max Fenig, had just died in a recent plane crash. ( "Tempus Fugit") While investigating the crash, Mulder learned that the doomed passengers of the plane, like he and Scully on their first case, had lost nine minutes immediately before the plane had crashed. ( "Tempus Fugit", "") Mulder consequently began to suspect that Max had been abducted off the plane before its crash, even though his deceased body was found soon thereafter. ( "Tempus Fugit")
In one of his closest encounters with extraterrestrials yet, Mulder discovered the body of a "Grey" alien beneath Great Sacandaga Lake. ( "Tempus Fugit") However, he was soon captured and arrested by the military on charges of interference with a military investigation into the crash of a commercial airliner. ( "Tempus Fugit", "Max") By the time he was released, Mulder had realized that Max Fenig had been carrying an object which constituted physical proof of the existence of alien life and intelligence. The object had been divided into three separate parts, one of which had been aboard the plane when it crashed and another part had also been taken. Mulder managed to obtain the third part and, although the object was highly radioactive, he attempted to transport it in a bag from an airport in Syracuse to Barnes Corners, New York. On the way there, however, the object was taken by a man who, like Max Fenig before him, was abducted off the plane. Mulder and the other passengers landed safely. ( "Max")
He and Scully later encountered Eddie Van Blundht, a man who had impregnated four women by making himself physically appear to be their husbands. The agents attempted to arrest Blundht, but his shape-shifting ability helped him to evade capture. While he was being pursued, Blundht changed his facial appearance to that of Mulder's. He later attacked Mulder and locked him in a hospital basement, while he assumed Mulder's lifestyle, even managing to fool Scully into believing that he was Mulder. Luckily, the real Mulder managed to escape from the basement and Blundht was later placed in the Cumberland Reformatory, where he was medicated with a form of muscle relaxant that stopped him from being able to change his facial appearance. When Mulder visited him one month later, Blundht remarked that Mulder was a "loser" and advised him to "live a little, treat yourself". ( "Small Potatoes")
Similarly to Eddie Van Blundht, Assistant Director Skinner soon also assumed Mulder's identity while secretly working to destroy evidence regarding the death of a female postal worker who had been fatally stung by bees. ( "Small Potatoes", "Zero Sum") As Scully was dealing with complications related to her cancer, Mulder alone investigated the postal worker's death and that of Dr. Valedespino, the expert in bees he had consulted six months before. Mulder believed that the bee attacks were related to the bees he had seen on the Canadian farmland earlier and discovered that the bees had been carrying the smallpox virus, a fact he had suspected but had never been able to prove. He finally also uncovered Skinner's involvement in the case, who explained that he had been trying to make a deal with the Cigarette Smoking Man in order to obtain a cure for Scully's cancer. ( "Zero Sum")
Around this time, Mulder contacted sixty-two year old Amy Anne Cassandra, who believed she was an alien abductee. He learned that she had been undergoing an experimental form of psychiatric treatment that had been effectively recovering repressed memories of her past. On April 10, 1997, Mulder drove to Providence, Rhode Island, where he submitted himself to the same form of therapy that Amy had been undergoing, hoping it would trigger his memory of the night his sister had disappeared. As part of the procedure, Mulder was subjected to light and sound that simulated an electrical impulse in his brain and was injected at the hip with a veterinary drug known to cause hallucinations, memory loss and blackouts. The drug caused Mulder to experience frequent painful seizures accompanied by vivid flashbacks to his childhood. He later witnessed Amy kill herself and her husband, David, using his gun. Covered in their blood, he drove David Cassandra's car to a motel, where he booked a room at about noon on April 11 and fell asleep alone in the room.
The next day, he awoke in shock with no memory of what had happened to him since two days before. He and Scully pieced together his previous two days but he was soon suspected of having murdered Amy and David Cassandra himself, and was consequently jailed. By the next day, Scully had determined that he was not responsible for the deaths and he was released from imprisonment. Mulder refused to be hospitalized because he believed that his seizures were helping him recall the events surrounding his sister's disappearance. They also made him question whether his real father was Bill Mulder or the Cigarette Smoking Man. Alone, Mulder returned to Dr. Charles Goldstein, the psychiatrist who had originally treated him, and requested for the operation to be completed. After his treatment, Mulder irrationally held Scully at gunpoint. He eventually acquiesced and his seizures ultimately subsided with no evidence of permanent brain damage. However, he was also left with no memory of the events that had led to Amy and David Cassandra's deaths. ( "Demons")
Later that year, Mulder's forensic anthropathologist contact, Arlinsky, notified him that a frozen corpse that seemed alien had been discovered in the Saint Elias mountain range, located in the Yukon Territory, Canada. At first, Mulder believed the supposed discovery of the frozen corpse was a hoax but, after he witnessed a limited physical examination on the corpse conducted at a warehouse in Sethburg, Virginia, Mulder came to believe that the discovery was genuine.
However, Scully introduced him to , an employee of the Department of Defense, who provided an astonishing story about how the conspiracy Mulder had been trying to unravel was actually an elaborate ploy by the government to cover up secret military experiments while leading the public to believe in aliens and UFOs. Kritschgau also claimed that the frozen body was a fake that would never be fully examined, as Mulder had only been meant to see it to encourage him to continue believing the lie that aliens existed. Mulder soon discovered that Arlinsky had been killed and that the frozen corpse had been removed from the warehouse, seemingly proving Kritschgau's story. ( "Gethsemane") Mulder was so immensely affected on an emotional level by having his entire belief system shaken by Kritschgau's claims that he seriously considered suicide. ( "Gethsemane", "Redux")
Kritschgau realized he had been followed after speaking with Mulder and Scully and called Mulder to warn that he was under surveillance. Mulder discovered he was also being spied upon, by a Department of Defense employee named . Moments after realizing that Ostlehoff had been spying on him from an apartment above his, Mulder shot the man in the face, simultaneously killing him and effectively removing his identity. In the same room where Ostlehoff had been shot, Mulder found a DOD clearance card and proof that he had been in contact with a member of the FBI for the last two months. Mulder believed that he and Scully may have been under surveillance since they were assigned to work together on the X-Files. ( "Redux")
Mulder, having effectively faked his own death (a feat that he once believed only Elvis Presley had managed to successfully accomplish), immediately contacted Scully. ( "Redux", "") He had Scully "identify" Ostlehoff's body as his own and used Ostlehoff's DOD clearance card to infiltrate the , where he began seeking a cure to Scully's cancer. With the assistance of Kritschgau, Mulder discovered rows of tables, each one supporting a body that appeared to be extraterrestrial. He also saw bodies of several women who had enlargened stomachs and lay on tables as irregular flashes of light illuminated them. Mulder later gained access to a large storage facility by a hallway connecting underground to the Pentagon. He took a vial with him before he exited, believing that it might contain a cure for Scully's cancer, but later discovered that it contained only deionized water. ( "Redux")
After revealing that he was alive and returning to the FBI, Mulder was told that Scully was dying as a result of her cancer. Acting on advice from the Cigarette Smoking Man, Mulder further analysed the vial and found a computer chip hidden within. Though thankful for the information, Mulder flatly refused an offer to leave the FBI and begin working for the Cigarette Smoking Man.
Although the FBI had evidence that Mulder had killed Scott Ostlehoff, he was told that he would be exonerated if he named the person at the FBI who Ostlehoff had been in contact with. Mulder was encouraged by Section Chief to call out Skinner as Ostlehoff's contact. However, on a hunch, Mulder instead called out Blevins as the FBI contact. Realizing that Blevins had been exposed, another member of the Syndicate shot and killed the Section Chief in his office. The Cigarette Smoking Man was also shot in his office around the same time and Mulder received news of his death. With the help of the computer chip that Mulder had discovered in the Pentagon storage room, Scully's cancer soon went into remission. ( "Redux II") She returned to working with Mulder.
He and Scully later traveled to a team seminar with two other FBI agents, Michael Kinsley and Carla Stonecypher, but they were stopped at a roadblock while driving through Leon County. At Mulder's request, he and Scully joined an investigation into several recent attacks that had taken place there, while their FBI companions continued to the seminar. Together with Scully and two local experts, Michele Fazekas and Jeff Glaser, Mulder helped search for an attacker in the Apilachacola National Forest. However, both local companions separately went missing when they were suddenly pulled under the foliage by one or more transparent creatures that Mulder saw and shot at. Mulder was also pulled to the ground but Scully caught sight of him struggling with an invisible creature and shot at it, freeing him.
The agents stayed in the forest through the night, during which Mulder suffered from cold related to shock. The next morning, he witnessed Scully fall down a hole into a network of caves and, as a creature approached him at ground level, Mulder jumped into the hole, painfully landing in a heap next to Scully. As a second creature in the cave prepared to attack the agents, Mulder warned Scully, who shot the predator. The agents were saved by Search and Rescue, aided by Agents Kinsley and Stonecypher, later that day. The second predator was never found. ( "Detour")
On December 23, 1997, Mulder rushed into his apartment as his phone was ringing. He answered the phone call, but there was no reply. ( "Christmas Carol") Mulder was unaware that the caller was Scully, who later contacted him after she discovered that a girl, Emily Sim, who had been living with adoptative parents, was actually her own daughter. ( "Christmas Carol", "Emily") In fact, Emily was a hybrid partially created from eggs that had been taken from Scully during her abduction. Emily had been used in secret experiments conducted by members of the Syndicate, who sent an alien bounty hunter to kill her after Scully and Mulder had discovered her existence. Unfortunately, Mulder was unable to stop the bounty hunter from succeeding. ( "Emily")
===1998===
In early 1998, Robert Patrick Modell escaped from confinement. Mulder attempted to search for Modell and Linda Bowman, the criminal's murderous sister. However, Mulder's judgment was impaired once by each criminal during the investigation. Suspecting that Modell's influence over Mulder might be more than temporary, Skinner tried to suspend him from active duty but Mulder resisted. Modell was ultimately killed by Skinner, and Scully later killed Linda Bowman. ( "Kitsunegari")
While pursuing Karin Matthews, a suspect who Mulder believed was capable of controlling nature, his car crashed into a fallen tree. Mulder narrowly avoided a branch that smashed through his car's windshield and, despite several bruises to his face, he managed to continue following the suspect on foot. 
Shortly thereafter, he became immersed in mud while trying to save Bobby Rich, a victim of Karin Mathews, from death. As Mulder and Bobby Rich continued to sink in the mud, a woodsman killed Karin Mathews and her influence on nature, as well as on the mud in which they were sinking, abruptly ended, allowing them to be pulled out of the mud. ( "Schizogeny")
Despite agreeing with Scully that they would both take a specific weekend off work, Mulder returned to the X-Files office and called his FBI partner soon after new information pertaining to one of the cases was discovered. He was unable to investigate the case, however, because Scully refused to return early from her vacation in Maine. She consulted him on a case she had discovered involving an outbreak of people acting involuntarily violent toward themselves but all of Mulder's suspicions regarding the case were incorrect. Mulder spent the rest of the weekend affixing pencils to the ceiling of the X-Files office, a fact that Scully discovered after she returned to work. ( "Chinga")
Soon after, Mulder was electrocuted several times by Esther Nairn using a taser to attack him. He later became trapped in a trailer crammed with electronics by an artificial intelligence program that strapped him to an upright harness. The program fed him illusory images of buxom blonde nurses, including one named Nancy, who operated on him, amputating his left arm and both his legs before he was ultimately freed by an illusory Scully. Mulder realized the images he was seeing were being generated by the artificial intelligence program but could not escape the illusory world it was creating until Esther Nairn and the real Scully eventually rescued him. ( "Kill Switch")
After Mulder apparently killed a boy he seemingly incorrectly believed was a vampire, he was extremely frustrated by the incident and became worried that he and Scully might even go to prison for their murderous actions. Eventually, however, Mulder and his FBI partner learned that the boy was still alive and that the town where he lived, Chaney, Texas, was full of people who, like the boy, had eyes that they could turn luminous green. Mulder was attacked by the town's residents and, although two victims had been found dead with two bite marks on each of their necks, the residents left Mulder still alive. After he regained consciousness, he discovered that his shoes, like those belonging to the previous two victims, were untied, linking the town's residents to the previous murders. They also abducted Scully around the same time but she and Mulder could find no sign of the residents after they recovered. ( "Bad Blood")
Mulder accepted an invitation to a Visiting Lecturers' Forum in the Massachusetts Institute, at which he publicly announced his loss of belief in the existence of extraterrestrials and revealed his conviction that those who did believe in alien life had been persuaded by a bombardment of lies concocted by the government. He later met Cassandra Spender, a woman who claimed to have been abducted by aliens on several occasions. She revealed that she had been inspired by the story of Mulder's encounter with Duane Barry and warned him that she expected to soon be summoned by aliens, believing that Mulder was the only person who could stop them from taking her. Although Mulder did not believe Cassandra's claims of abduction experiences nor that she would again be taken, he and Scully were warned by her son, , a young FBI Special Agent who hoped to build a good impression within the Bureau, against listening to her stories. Mulder later learned of two incidents in which many victims had been burned to death on Skyland Mountain - where Scully had been taken by Duane Barry - and in Kazakhstan. Shortly thereafter, Mulder discovered that both Scully and Cassandra Spender had suddenly disappeared. ( "Patient X")
He later discovered that they had been at another mass burn site, this time on a bridge above Ruskin Dam. There, Scully was found alive but with no memory of what had happened to her. Cassandra Spender was still missing, though Mulder believed she would ultimately be found. At his suggestion, Scully underwent hypnosis, during which she seemed to vividly recall witnessing an alien ship destroy faceless men who had set fire to several victims surrounding her and Cassandra Spender, who had then apparently been lifted up in the air by the same alien ship. Mulder suspected that Scully's memories were an interpretation of a very powerful event, staged by the military, and that Cassandra Spender had been taken aboard a military aircraft.
He was later attacked by Krycek, who revealed that one of the warring alien races planned to colonize the planet unless Mulder opened his eyes to the truth. Krycek also revealed that the mass burn sites were destined to serve as alien "lighthouses" for the invasion, but had been used as battlefields where alien rebels had struck abductees as an attempt to upset plans for the occupation of Earth. Krycek tasked Mulder with freeing one of the alien rebels from an airforce base but, realizing that the rebel was aboard a military truck leaving the base, Mulder boarded the vehicle himself. However, another alien rebel abducted both the rebel prisoner Mulder was attempting to rescue and the driver of the truck, an alien bounty hunter loyal to the colonization plans. Mulder's belief in the existence of extraterrestrials had come full circle and he now realized that the aliens planned to colonize the planet. ( "The Red and the Black")
Despite the changes in his beliefs, Mulder was never referred to as "skeptical" until a detective remarked that he was, while Mulder was trying to prevent Marty Glenn, a 28-year-old blind woman who seemed to have murdered two victims, from being sent to prison. Mulder single-handedly proved that Marty's estranged father, Charles Wesley Gotts, was the actual murderer, but Gotts was later killed by Marty, who was consequently sent to prison. ( "Mind's Eye")
While tailing a possible suspect, Mulder became involved in helping Scully to conduct an unofficial search for several missing girls. ( "All Souls")
As a result of broadcasting his feelings about the government and their conspiracies against the American people at the UFO conference, Mulder was contacted by a militia group called the New Spartans. He infiltrated the group as part of a classified, deep-cover assignment. In order to gain the trust of the group's second-in-command, Jacob Steven Haley, Mulder was forced to let Haley commit murder with a bio-toxic weapon. When Haley grew suspicious that Mulder was spying on the group, he was interrogated by Haley and a bald man who broke one of Mulder's fingers before Haley finally announced that he believed Mulder. In Mulder's apartment, he and Scully talked openly about his infiltration of the group, unaware that the group's leader, August Bremer, was listening in to their conversation. Mulder was later forced to help the group commit an armed bank robbery. Despite Haley's belief that Mulder was not spying on the group, Bremmer convinced him otherwise by playing an audio recording of Mulder's discussion with Scully. However, Bremmer, who was actually working for the CIA, secretly freed Mulder, telling him never to return. ( "The Pine Bluff Variant")
When later assigned the task of performing a threat assessment for VinylRight, a Chicago company which had received an audio-taped manifesto that spoke of a monster stalking employees, Mulder complained to Scully that the assignment was not worth their time. ( "Folie à Deux") By then, Mulder's fingers had been taped to help them heal after his last assignment. ( "Folie à Deux", "The Pine Bluff Variant") Mulder decided to investigate VinylRight alone, without Scully's assistance, and used his previous experience transcribing wiretap tape to study the recorded manifesto. ( "Folie à Deux", "", "The Host", "Sleepless")
After learning that the case might be related to a former X-File, he asked Scully to help him perform the threat assessment. Before she could reach him, however, Mulder was taken hostage by VinylRight employee Gary Lambert, who had recorded the manifesto believing that his boss, Greg Pincus, was a monster. Lambert managed to convince Mulder that Pincus was indeed a monster but was shot and killed by a SWAT team soon after. To such an obsessive degree that he angered Skinner, Mulder searched for proof that Pincus was a monster, discovering that the situation was related to five previous X-Files. However, believed to be delusional, Mulder was restrained in a psychiatric ward of a hospital, where he believed he was visited by the monster. He was rescued by Scully, who shot the creature as it fled, but she and Mulder were later unable to locate Greg Pincus. ( "Folie à Deux")
Mulder was reunited with Diana Fowley, his former girlfriend and FBI partner, after she requested reassignment to Washington, D.C.. Together with Fowley, Scully and Agent Jeffrey Spender, Mulder worked on investigating the shooting of an adult male chess champion in Vancouver. He correctly suspected that the man's opponent, a boy named Gibson Praise, had been the real target and that Praise was telepathic. Suspecting that Gibson Praise might be the key to understanding everything in the X-Files, Mulder suggested that the shooter be given immunity from prosecution in exchange for information. However, both Skinner and Diana Fowley worried that the X-Files might be shut down once again, if the agents investigating the files drew the wrong kind of attention by requesting the shooter's immunity.
After interviewing the shooter, Mulder came to the conclusion that Gibson Praise' telepathic ability was due to the fact he was part alien. Soon after this realization, Mulder discovered that Gibson Praise had been kidnapped and that Diana Fowley had been hospitalized in critical condition after having been shot while trying to protect Gibson. Mulder also learned that Gibson's shooter had been murdered in his cell by the Cigarette Smoking Man or someone working for him. As he had seen Agent Spender meet with the Cigarette Smoking Man earlier, Mulder approached Spender at FBI Headquarters and accused him of having killed the shooter.
Mulder was soon informed of talks that were being held on the issue of reassignment for himself and Scully that included instructions from the Department of Justice to close down the X-Files. Although Mulder believed that the situation he and Scully now found themselves in had all been planned without his knowledge, Scully told him that it might no longer matter what he believed as the forces against them seemed to have won. Later, Mulder received news of a fire within his basement office. He and Scully returned to the FBI's Headquarters, where they saw that the office containing the X-Files had been severely incinerated in the fire. All information pertaining to the cases they had worked on over the past four years had been apparently destroyed and lost forever. ( "The End")
Category:Events