Season 10

S10E1 · My Struggle

The episode opens with a monologue by Fox Mulder detailing alien-related events in history, leading up to his partnership with Dana Scully and their investigations into the X-Files. The subsequent scene takes place in 1947, when an unnamed military doctor is escorted by a Man in Black via bus to the site of a crashed spacecraft in the New Mexico desert. After viewing the wreck in amazement, the doctor finds a trail of blood leading to a wounded being, ostensibly an alien, crawling away from the scene. Despite the doctor's pleas, soldiers shoot and kill the alien.

Moving to the present day, fourteen years after the closure of the X-Files and seven years after the events of I Want to Believe, Mulder is contacted by Scully at the behest of FBI Assistant Director Walter Skinner, who wants him to meet a right-wing online webcaster named Tad O'Malley. Mulder and Scully reunite in Washington, D.C., where they are picked up by O'Malley in his limousine and driven to a remote farmhouse in Low Moor, Virginia. Inside, they meet a young woman named Sveta, who claims to have fragmented memories of having her fetuses stolen from her during alien abductions and to possess alien DNA, which Scully agrees to examine. O'Malley takes Mulder to a secret location where a triangular aircraft built from alien technology is being housed. The craft is referred to as an "ARV", or Alien Replica Vehicle.

During her medical examination, Sveta makes several astute observations which allude to Scully's strained relationship with Mulder, making Scully uncomfortable. When the test results on Sveta's blood come back, Scully immediately orders the sample re-tested. Meanwhile, Mulder meets with the now-aged doctor from the New Mexico crash site, a man he has known for 10 years. Mulder offers the doctor a new theory based on the "ARV", Sveta's memories and past hints from the doctor: Mulder now believes that Colonization and the alien invasion were all an elaborate hoax to distract.

Instead, Mulder thinks it was a "conspiracy of men" who have used extraterrestrial technology on human parties for decades, and these events were subsequently made to look like alien abductions. Mulder outlines a global conspiracy involving the hoarding and testing of alien technology which will be utilized at some future point to stage an attack on America and eventually take over the world. The doctor refers to Mulder's previous belief in Colonization as "nonsense" and says that Mulder is now close to the truth, but refuses to disclose the purpose behind the abductions and the tests on human subjects.

Following these revelations, Mulder shares his theory with Scully that the conspiracy is a group armed with alien technology attempting to subvert society and assume power over the world. Before O'Malley can go public with his claims, his website is shut down, the "ARV" craft is destroyed and its scientists are killed by heavily armed men dressed in military uniforms, and a UFO intercepts Sveta while she is driving, she attempts to escape but is killed when her car is destroyed in an explosion. Mulder and Scully meet in a dark parking garage and Scully reveals that Sveta's re-tested DNA sample confirms that she does in fact possess extraterrestrial DNA; a test Scully has performed on herself has revealed that she does as well. Mulder states that Sveta is the key to exposing the conspiracy and those responsible. They then receive an urgent summons from Skinner requesting them to meet him.

The episode ends revealing the Cigarette Smoking Man alive in the present day, receiving word via telephone that the X-Files have been re-opened.

S10E2 · Founder's Mutation

At the headquarters of Nugenics Technology, researcher Dr. Sanjay arrives at work in a troubled state, hearing a mysterious high-pitched noise in his head. At a staff meeting, the noise becomes so overwhelming that he flees and locks himself inside a server room, where he begins frantically deleting data. Desperate to stop the noise, he shoves a letter opener through his eardrum and into his brain, killing himself. Before doing so, he writes something on the palm of his left hand.

With the X-Files now re-opened by the FBI, reinstated agents Fox Mulder and Dana Scully are dispatched to investigate the incident. Receiving little cooperation from Nugenics, Mulder steals Sanjay's mobile phone and contacts the last person he called. At a Washington bar, he meets a man named Gupta, Sanjay's secret lover. Gupta tells Mulder that Sanjay had expressed concern that his "kids" were dying. Meanwhile, Scully performs Sanjay's autopsy and finds the words "founder's mutation" written on his left palm – a reference to Nugenics' reclusive owner, Dr. Augustus Goldman, known to employees as "The Founder". Upon searching Sanjay's apartment in Dupont Circle, the agents discover several photographs of horribly disfigured children. Police arrive, and Mulder suddenly becomes overwhelmed by the high-pitched noise which afflicted Sanjay. The sound somehow conveys the message "find her" to Mulder.

Upon presenting their findings to Assistant Director Walter Skinner, Mulder and Scully are told that the case has been closed in order to placate the Department of Defense, which has ties to Goldman and Nugenics. Privately, however, he tells the agents to continue. Observing footage of birds which flocked near the Nugenics building at the time of Sanjay's death, Mulder thinks that the noise is a frequency normally unheard by humans. Citing Nugenics' reluctance to assist in the investigation, the agents visit the hospital where Scully works in order to find Goldman, who happens to be one of the hospital's biggest donors.

They are approached by a young woman named Agnes, who expresses a desire to leave and claims her unborn child is abnormal. Outside, Mulder and Scully discuss the possibility that Goldman is experimenting on pregnant women for The Project, and reminisce about their son William, who remains in hiding. Later, Scully has a fantasy about living with William, shown as a teenager going to school, having an accident, and having alien, lizard-like black eyes.

The agents receive approval to meet Goldman, who purports to conduct research on children suffering from debilitating genetic conditions such as Proteus syndrome, Crouzon syndrome, epidermal dysplasia, Pitt-Hopkins syndrome, ichthyosis, and Marfan syndrome. During a tour of his facility, they witness a confrontation in which one of his patients causes objects to move on their own. Soon afterward, they learn that Agnes has been struck and killed by a car, with her fetus mysteriously missing. The agents next question Goldman's wife Jackie, who has been confined to an insane asylum and claims her husband is keeping her there against her will.

She recalls an incident in which her young daughter fell into a swimming pool and was thought to have drowned after spending ten minutes submerged. Jumping into the water, Jackie was shocked to find her daughter instead breathing normally underwater. Realizing that Goldman experimented on her while pregnant, she fled but wrecked her car. Under attack by the noise – her unborn child's attempt to communicate with her telepathically – Jackie cut her uterus open with a kitchen knife; the baby escaped and was presumed dead.

Using security footage, Mulder and Scully discover that a Nugenics janitor working one floor directly beneath Sanjay reacted strangely at the precise moment of his suicide. They drive to the remote home of the janitor, Kyle Gilligan, and are confronted by his adoptive mother. Mulder is once again incapacitated by the noise. Noticing a nearby flock of birds, Scully quickly locates Kyle, forces him to stop, and takes him in to custody. Kyle reveals that he killed Sanjay unintentionally and demands to meet his sister, who is one of Goldman's test subjects.

Kyle is taken to Goldman's lab, where he is presented with a girl who Goldman claims to be his sister. However, Kyle quickly realizes that the girl is a decoy and not his actual sister, and he runs down the corridor where he encounters the irate patient from earlier – his real sister, Molly. After speaking to each other telepathically, the siblings use their abilities to repel the agents. Utilizing the noise, they kill Goldman and flee the Nugenics building.

S10E3 · Mulder and Scully Meet the Were-Monster

When a dead body is found with its throat ripped open in the woods outside Shawan, Oregon, Dana Scully and Fox Mulder are called in to investigate whether it was an animal attack, a serial killer or just maybe a strange creature as described by eyewitnesses. Mulder continues to question his faith in the unexplained as he attempts to gather proof of the existence of the new creature he and Scully investigate before jumping to conclusions. During an inspection of a truck stop, Mulder, Scully, and an animal control officer named Pasha (Kumail Nanjiani) seemingly encounter the creature.

Eventually, evidence starts to coalesce, and Mulder begins to suspect that an individual named Guy Mann (Rhys Darby) is actually a murderous were-monster, capable of transforming into a lizard person. After confronting Mann, his suspicions are proven only half correct: Mann is not a man who turns into a lizard person, but rather a lizard person who turns into a human. Mann apparently became a shape-shifter after being bitten by a human some days before and laments the existential hopelessness of human life, full sentience, and modern society. In the end, it is revealed that Pasha was the true killer, and that Mann was simply in the wrong place at the wrong time.

Upon learning this, Mulder rushes to tell Mann, who quickly brushes off the news. He informs Mulder that he will be going into a 10,000 year hibernation, but that he was glad to have met Mulder. Then, before Mulder's eyes, Mann turns back into his original lizard person form and scampers off into the night. Mulder thus witnesses a paranormal happening, and his faith is renewed.

S10E4 · Home Again

Mulder and Scully are sent to investigate the murder of a city official, which it seems no human could have committed. At the crime scene, Scully receives a phone call from her older brother Bill, in Germany, telling her that their mother had a heart attack, causing her to leave and visit her. At the hospital, she again receives another call from her older brother asking for his mother's condition, and also learns that her mother had changed her living will, stating not to attempt resuscitation if she is unconscious or on life support.

Mulder then meets Scully, who tells him that her mother had asked for Charlie before falling into coma and had changed her living will without consulting. Shortly afterwards, her mother is extubated and Scully receives a phone call from her younger brother, Charlie, who talks to their mother on speaker. Upon hearing Charlie's voice, her mother suddenly opens her eyes and then holds Mulder's hands and says "my son is named William, too", dying shortly afterwards.

Back at their investigation, Mulder and Scully then track down a mysterious creature known as the Band-Aid Nose Man. He is a force of destruction — ripping bodies apart — but the cause of the rage is complicated. The creature is the inadvertent creation of a street artist named Trashman, who drew the image of a defender of the homeless. Trashman claims the Band-Aid Nose Man is a " thought form ". Meanwhile, Scully has flashbacks about her and Mulder's child, William, who was placed for adoption for his protection.

After identifying city official Landry as the last victim, Scully, Mulder and the Trashman head to Franklin Hospital to prevent him from being killed by the Band-Aid Nose Man. There, Landry starts smelling a very unpleasant odour and goes to an off-limits corridor, where he is confronted by the creature. He tries to flee, and in doing so, he enters a room where he is attacked by the creature. Seconds later, the agents and the Trashman arrive in the room, only to find Landry's dismembered body and no signs of the creature, prompting Scully to question how the creature left the room, given there is only one exit door and Landry's shouts were heard a few seconds ago.

The episode ends with Mulder and Scully at a beach talking about Scully's interpretation of her mother's dying words, where she tells Mulder that her mother had asked for her brother, despite him being out of her mother's life, because her mother was responsible for him, as they, Mulder and Scully, are for their son, William.

S10E5 · Babylon

In Texas, a young Muslim man prays and goes about his daily routine. After driving to a motel to meet a friend, they then head over to an art gallery called Ziggurat for an art opening, which is later revealed to have been showcasing controversial depictions of Muhammad considered offensive to Muslims. Prior to leaving the car, they hold hands and say a prayer and then walk into the gallery, which shortly thereafter explodes. One of the men, now presumed to be a suicide bomber along with his friend, survives but is incapacitated in a vegetative state. Meanwhile, other bombers are shown to be planning another attack.

Back in Washington, D.C., Mulder and Scully meet Agents Miller and Einstein, both younger counterparts to the agents (believer and skeptic) but Miller is more extreme. While Agents Miller and Einstein leave to solve the bombing in Texas, Mulder asks Einstein (instead of Scully due to her recent loss) to meet up with him while Scully meets Miller in Texas.

Mulder and Einstein's relationship starts off rocky due to Einstein's extreme skepticism. Scully and Miller get along well but clash with bigoted Homeland Security agents who try to silence him. The agents try to find a way to communicate with the vegetative bomber. Miller, who had worked with the FBI in Iraq, tries to speak with him in Arabic, while Scully checks his EEG for any subconscious reaction.

Arriving in Texas, Mulder comes up with an idea to communicate with the comatose bomber. Einstein gives Mulder psilocybin mushrooms, making Mulder high. He wanders into a rodeo themed bar where he dances and passes out after seeing The Lone Gunmen amongst the crowd. In his dreams Mulder is on a ship being beaten by the Cigarette Smoking Man. He sees the comatose man in his mother's arms. He speaks to Mulder in Arabic.

Mulder wakes up in a hospital and is scolded by Skinner. Einstein reveals that she had given Mulder a placebo, despite Mulder's objections considering his powerful and profound experience. Mulder later spots the bomber's mother hoping her presence would wake him up. However, the man dies. Agent Miller asks Mulder about his dreams, after trying to remember Mulder says, " Babil al funduq " which turns out to be the name of the hotel where the other bombers are hiding, Babylon Hotel. FBI SWAT agents arrive at the hotel and capture the bombers.

Mulder later questions human nature and their beliefs, but then hears a loud sound of trumpets, suggesting it is the voice of God.

S10E6 · My Struggle II

The investigations that Mulder and Scully previously began with conspiracy theorist Tad O’Malley have awakened powerful enemies. A widespread panic begins as people all over the country suddenly start falling gravely ill, and Scully must look within to try and find a cure. Meanwhile, Mulder confronts the man whom he believes to be behind it all, but another figure from Mulder and Scully’s past may prove to be the key to their salvation.