An experiment in dark matter accidentally turns a scientist's shadow into a deadly weapon that can unzip a person's molecules if they are touched by it.

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.

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".

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.

After the body of a decapitated EMT disappears from the morgue and an identical man starts work at the same hospital, Mulder believes that the man has the ability to regrow parts of his body, including his head. The agents soon discover that Betts' body is riddled with cancer and he is able to live in that condition but needs to feed on cancerous tumors to keep up his strength.

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.

Five babies in the same town are all born with tails and the local OB-GYN is blamed for tampering with fertilized eggs. However, Mulder discovers the culprit to be a simple man with a genetic deformity who may have the ability to alter his appearance.

Set in 1989, the story of the founding of The Lone Gunmen is finally told as we see how a straight-laced federal employee, a sex mad AV expert, and a nerdy computer hacker meet Susanne Modeski, a strange woman with evidence of a government conspiracy. When their plan to expose the conspiracy fails and Susanne is captured by a group of men-in-black, led by none other than X, they soon become a paranoid group of government watchdogs.

On her Christmas vacation with her brother's family, Scully receives a mysterious phone call from a familiar voice who says, "She needs your help. Go to her." The phone call leads Scully to a murder case where the victim's 3-year-old adopted daughter bears an uncanny likeness to her sister, Melissa, at that age. The emotional roller coaster that follows has Scully believing that her sister had a baby during a period when she traveled the country and she tries to adopt the child, knowing that caring for the little girl would change her life.

DNA testing on Emily reveals that she is actually Scully's daughter and Mulder comes to assist her. While Mulder is looking for any information about where and how the girl was born, Scully searches for a cure to Emily's strange illness.

Pusher returns as Robert Patrick Modell escapes from the mental hospital and the FBI promptly organizes a manhunt, assuming that he will continue where he left off. But is he really trying to get revenge on Mulder, or does he want to warn him of another evil?

After Mulder chases down and kills a young man who he believes to be a vampire, the agents return to DC aware of the mistake they just made. Faced with a lawsuit from the family of the man, they recount each of their sides to the story leading up to the event. In the extremely humorous stories that follow we see how Scully and Mulder both perceive each other.

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.

While being detained near the famed "Dreamland" Area 51, a strange craft flies overhead and Mulder swaps bodies with an Area 51 "Man-in-Black". While the other agent has fun in Mulder's body, Mulder himself finds it difficult to fit into someone else's life, especially a shadowy one. Mulder contacts Scully about the body swap and tries to get her the flight data recorder from the UFO test flight, but his alter ego uses Mulder's FBI persona to have him arrested.

Mulder is thrown in jail at the Area 51 compound but is released when it is discovered that the flight data recorder he stole was a fake. Scully comes to her senses and realizes that the Mulder she sees isn't who he really is and heads back to Nevada to help the real Mulder. Meanwhile, the mechanism that caused the body swap is rapidly snapping back, undoing everything in its wake, and Mulder and his alter ego must race to put themselves back where they belong.

Assistant Director Kersh tries to tear Scully and Mulder apart when he partners Scully with a New York agent investigating Alfred Fellig, a freelance police photographer who conveniently shows up to document the scene of a death as soon as it happens.

While the young hotshot agent is convinced that Fellig is murdering the people, Scully has other (paranormal) theories.

A woman is forced to relive the same day over and over as she tries to prevent Mulder and Scully from being killed by her boyfriend during a bank robbery attempt. As the events restart again and again, Mulder's sense of Deja-vu grows stronger.

While on a stakeout of a Government Defense Convention in Las Vegas, The Lone Gunmen are reunited with Susanne Modeski, the mysterious woman who disappeared ten years earlier when they first met Agent Mulder.

When the bodies of a couple who have been missing for less than a week are discovered to have been reduced to bone, Mulder suggests that recent paranormal phenomena in the area may have caused the accelerated decomposition.

A monster who feeds on human brain matter tries to lead a normal life, but he soon cannot control his feelings of hunger.

As the year 2000 draws closer, the agents are up against a man from the Millennium Group who believes that he can bring about the end of the world on the 31st of December if he resurrects four former members from the dead. To gain more insight into the group and its practices, Mulder and Scully enlist criminal profiler Frank Black to assist them in the investigation.

When a small-time magician performs a trick where it appears that he turns his head all the way around but is then found in his van dead with his head neatly sawed off, Mulder and Scully suspect he was murdered and get caught up in an intricate scheme planned by two magicians trying to rob a bank.

A Los Angeles police officer who is being filmed for the show COPS is attacked by a strange monster and Mulder and Scully are investigating the case. Scully is wary of having their faces put on national television but Mulder welcomes the publicity.

Mulder and Scully suspect that hexcraft is the source of threats against a doctor's family.

Mulder and Scully discover a genie in a rug who, after 500 years of granting wishes, has come to the conclusion that people are still as greedy and self-centered as they always have been, and she begins to corrupt the wishes she grants if they are not specific enough.

Scully evades Doggett's help in investigating a vicious murder in a remote area of Utah, and she is trapped in the small town by a religious cult that believe a slug-like creature is the second coming of God who needs a human host to survive.

Scully and Reyes join forces to try and find Doggett when he goes missing. Doggett has his own problems, having woken up in jail in Mexico suffering from amnesia. With no knowledge of who he is, Doggett is befriended by a local who soon has him working smuggling illegal immigrants across the border.

The agents ask the Lone Gunmen to help find their friendly foe Yves Adele Harlow after former Area 51 Man-In-Black Morris Fletcher claims she is one of the super-soldiers.

Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. The house is owned by a man named Oliver who is obsessed with the show and has rigged the house into a series of traps and changing appearances to look like the Brady house.