Відбувається серія сексуально орієнтованих вбивств, які є ідентичними, за винятком того, що свідки описують підозрюваного то як чоловіка, то як жінку. Розслідування приводить Скаллі та Малдера до спільноти людей амішського типу під назвою Споріднені.

Малдер неохоче приймає нового напарника, агента Алекса Крайчека, з яким йому доведеться розслідувати смерть кількох солдатів з підрозділу «Зелених беретів», які брали участь в експерименті з позбавлення сну під час війни у В'єтнамі.

Жінка детектив таємничим чином виявляє останки агента ФБР, який зник у 1940-х роках під час розслідування справи про вбивство, подібної до тієї, якою зараз займається вона. Малдер і Скаллі вважають, що первинний вбивця передав свою генетичну схильність до насильства своєму онукові.

Під час розслідування кількох смертей і вбивств у таборі гаїтянських біженців Малдер і Скаллі потрапляють у єпіцентр таємної ворожнечі між начальником табору та священиком Вуду.

Інопланетний мисливець за головами викрадає Скаллі та хоче обміняти її на сестру Малдера, яка, як виявляється, сама є клоном. Після того, як обмін йде не за планом, і Малдер дізнається правду про Саманту, він вистежує мисливця за головами до його корабля, похованого в арктичних льодах, і вимагає розповісти, де знаходиться його справжня сестра.

Коли половина екіпажу корабля ВМС залишає свій човен у рятувальному плоту і через 18 годин їх рятують, вони виглядають приблизно на 60 років старшими, ніж вони повинні бути. Малдер припускає, що корабель потрапив у часову аномалію, яка прискорює їхнє старіння.

Коли хвороба, схожа на чуму, вбиває десять чоловіків у в’язниці суворого режиму, Скаллі намагається потрапити на карантин і з’ясувати причину та походження зараження, а Малдер і група маршалів США вистежують двох втікачів, які можуть бути заражені.

Після кількох зникнень у маленькому містечку, Малдер і Скаллі проводять розслідування і знаходять у річці сотні людських кісток. Вони дізнаються, що чоловік, який стоїть за головним джерелом багатства міста - заводом з переробки курятини, знайшов спосіб продовжити своє життя за допомогою канібалізму.

A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.

After a suicide attempt and multiple murders at a military hospital, Mulder and Scully meet a quadruple amputee who has gained the power of astral projection and is taking out his personal frustrations on his commanding officers.

Mulder is trapped inside a train car which contains a suspected alien-human hybrid and also a bomb, while Scully pursues the truth about her abduction and the mystery behind the implant in her neck.

A rare planetary alignment causes strange behavior in the residents of a small town, but particularly in two teenage girls who were born at the exact same moment on that date. While investigating the strange occurrences Mulder's interest in the local female detective makes Scully jealous.

A French salvage ship searching for a lost WWII fighter plane unknowingly surfaces an alien which appears in the form of black oil and has the ability to jump hosts. Mulder heads to Hong Kong to investigate the salvage broker who sold the information to the French and he encounters Krycek, who has been selling information from the MJ documents. As Mulder prepares to take Krycek back to the US, the alien makes its way to Hong Kong and takes control of Krycek.

Mulder and Scully are asked to help in a case involving Robert Patrick Modell, a murderer possessing the psychic ability to force his will onto people. Due to a brain tumor that is slowly killing him, he is searching for a "worthy adversary" and forces Mulder into a battle of mind over matter.

A alien abduction of two teenagers with endless versions of the same story prompts a science-fiction novelist to to write a book about the incident; however, nobody involved with the investigation can tell him the full story with any accuracy.

Mulder and Scully investigate a series of murders linked to a mysterious device that alters television signals causing paranoid hallucinations. One of them falls victim to it.

Several kidnappings of young women linked by distorted photographs lead Mulder and Scully to a man who can imprint his darkest fantasies onto undeveloped film and is trying to save the women from the "howlers".

After an FBI raid on a doomsday cult called the "Temple of the Seven Stars", Mulder meets Melissa, a cultist who claims to have known him in a previous life during the American Civil War. Scully believes the woman is a delusional schizophrenic, but Mulder allows himself to be drawn into her fantasies.

Mulder is given a tip about potentially dangerous paramilitary operations on the U.S. soil but during the sting operation is surprised to find out the identity of his mysterious informant - it turns out to be Alex Krycek. Suspicious about his true motives, Mulder reluctantly follows the information provided by Krycek. However, soon he discovers a much bigger conspiracy which takes him to a gulag in Tunguska, Russia where prisoners are being used for experiments involving a substance of alien origin.

While imprisoned in Russia and infected with the Black Cancer, Mulder learns that Krycek is working with the men responsible and everything has been a setup from the start, while Scully and Skinner are called to a suspicious Senate hearing where the only question is the whereabouts of Agent Mulder.

Mulder's dreams help him in finding the body of a little girl which reopens one of his old cases in the Violent Crimes Unit. This leads him to believe that the killer he captured had more victims and that Mulder's sister Samantha may have been one of them.

While Mulder is forced to take a vacation he leaves Scully with an assignment to keep her busy until he returns. However, she decides to start living and goes on a date with a man who believes that his tattoo talks to him and is telling him to stay away from other women.

Scully's recent failing health is revealed to be an inoperable cancer in her skull, which appears to be common among abductees and she attempts to come to terms with her condition. Meanwhile, Mulder and the Lone Gunmen break into a high-security research lab to find the cure that could save her life.

While celebrating Scully's 33rd birthday, a strange woman informs Mulder that NICAP member Max Fenig (see Fallen Angel) has recently died in a plane crash. After a visit to the crash site and finding Max's body with radiation burns on it, Mulder suggests that the plane was intercepted by a UFO and is rapidly being covered up by the military.

A super-intelligent virus program is let loose on the internet and begins to grow and expand by itself, eventually killing its creator when he tries to eradicate it.

Scully faces her Catholic faith and the loss of her daughter Emily when she is asked to help a family whose adopted daughter was found dead in a position that looked like she was struck down by God himself.

Scully fears that Mulder has gone to the other side when she sees him assisting a federal suspect escape custody. In truth he has infiltrated a terrorist group testing a deadly biological weapon that can eat through a person's flesh.

Mulder is held hostage inside an office where a man claims his boss is a monster and has clouded all their minds while he turns them into zombies one by one, which is disbelieved until Mulder opens his mind and allows himself to see it too.

Mulder is trapped in a car with a man who has developed a serious ear condition which can only be suppressed by driving west at high speeds. As Scully tries to find the cause and a cure for the problem, Mulder and the man get closer and closer to the ocean.

After a scan of a couple's unborn child is found to have strange growths protruding from the head and back, the fetus is taken from inside the mother by a demon creature while she is asleep. Mulder heads to investigate after Agent Spender dismisses the claims, and discovers that the father is actually a demon who wants to have a normal child.

The Cigarette-Smoking Man reveals all the government secrets from the past 50 years in order for his son, Jeffery Spender, to join him in his work. Mulder learns that the final stage of the conspiracy will soon begin with the hybridization of the Syndicate members, and he must stop it from happening. Agent Spender deceives his father and arranges for Mulder and Scully to be reassigned to the X-Files, which doesn't sit too well with the Cigarette-Smoking Man.

Arthur Dales summons Mulder and Scully to his holiday home in Florida where he is concerned over the disappearance of his neighbors. Despite the raging hurricane, Mulder and Scully head out to investigate and discover several strange deaths caused by an octopus-like sea creature that swam in through the overflowing sewer system.

After a tornado rips through a prison camp, one of the inmates disappears from solitary confinement and the prison warden is killed. As Mulder and Scully track him, he appears to have the power to pass through solid matter while changing its composition.

Two scientists confer about each of their metal objects that were found in Africa and they theorize that the objects are pieces of a puzzle which could be undeniable proof that human, plant, and animal life did not originate on this planet. When one of the scientists is killed and the objects are stolen, the agents investigate and Mulder begins to experience severe neurological pain caused by the objects.

Reverend Orison hopes to save Donnie Pfaster's soul by helping him break out of prison, but Donnie immediately plans to go after the victim that once escaped him... Scully.

The Cigarette-Smoking Man offers to show Scully the cure for all diseases if she travels with him, but on one condition: Mulder must not know about her trip.