The X-Files have now been officially closed down and Mulder and Scully have been reassigned to different positions. Scully has been assigned as an instructor at the FBI Academy while Mulder is doing menial surveillance work. It is at this time that Mulder is contacted by his friend in the Senate who tells him to go to Puerto Rico to find evidence of alien contact at the large satellite array located there.
When several men are found dead in New Jersey with the same strange looking bite marks on their bodies, Skinner orders Mulder to investigate. Mulder discovers a genetically mutated creature that is stalking its victims in Newark's underground sewer system.
In a small western Pennsylvania town, several mild mannered residents suddenly go berserk. Mulder believes that it is more than coincidence when he investigates claims that the suspects receive written messages to hug in their digital displays of their household appliances.
Via a new source, Mulder receives a tape of a 911 call made by a man in New York City who said that his Lexington Avenue apartment building was on fire. The apartment buidling, however, had not caught on fire, yet the man had died from internal injuries associated with being burned in a fire. Mulder tries to open a case file on it, but is beaten to the punch by another agent, and his new partner, Alex Krychek.
Mulder is called to a hostage situation involving Duane Barry, a former FBI Agent who claims to be an alien abductee and wants to get back to the abduction site with someone who will be taken instead of him. Unfortunately, the someone he eventually chooses is Scully.
When Mulder finds out that Scully was kidnapped by Duane Barry, he risks the wrath of his superiors and the annoyance of Agent Krycek in order to do whatever it takes to find her. Meanwhile, Krycek is found to be reporting Mulder's activities to the Cigarette-Smoking Man.
The X-Files have been reopened and Agent Mulder flies to Hollywood to investigate a series of vampire like murders in which victims are drained of their blood and puncture wounds are found on their bodies. Mulder meets and falls for a mysterious woman although, she is a prime suspect.
Scully mysteriously reappears in a Washington hospital, alive but in a coma. Knowing that she had signed a last will and testament wishing to end her life if she was in such a state, Mulder works against the clock and looks for evidence on who did this to his partner and how he bring her out of the coma.
With Scully back in the X-Files, Mulder and her flies to the site of an erupting volcano in Oregon to investigate the mysterious disappearances of several scientist who were studying the volcano. Mulder and Scully discover a deadly life form that can survive in the searing heat of the crater and is killing the scientists to avoid being discovered.
While investigating the connection between the abduction of several teenagers and a rural religious cult, Mulder and Scully discover a secret test being performed on the children using the "Purity Control" alien DNA from 'The Erlenmeyer Flask' which leads Mulder to "the crew-cut man", Deep Throat's murderer.
Mulder and Scully investigates strange occurrences in an old-age care home when one of the nurses is attacked by unseen supernatural forces. Both agents come in contact with the unseen forces, which seem to surround several elderly residents.
A young female police detective, who has been having visions of an unknown hug, inexplicably discovers a body buried in a remote field that belongs to an FBI agent killed over 40 years ago. As the detective continues to have visions, Mulder and Scully trace the agent's movements to an investigation into a murderer who had been put away for attacking a woman fifty years ago.
A female inactive person, dug-up and mutilated, is brought to Mulder's attention by a Minnesota agent claiming it as the work of aliens. Mulder, however, suspects the desecration is done by a fetishist and has the agent put out a warning to all law enforcement agencies in the area. At the same time, Scully begins to feel intensely uncomfortable with the work of the predator and his prey.
Some teenagers feign an occult ritual in an attempt to score, but cause the death of one of them instead. Mulder and Scully are called in to investigate, but the town's real worshippers attempt to hide their tracks.
When a soldier who was stationed at a resettlement camp for Haitians, drove himself into a tree, Mulder and Scully are called to investigate by the grieving wife. Mulder and Scully then, found themselves in the middle of a secret war between the camp commander and a Voodoo priest.
A newspaper ad placed to locate a certain doctor sets off the hug of several people with the same face. When Scully and Mulder locate another look-alike, they must reach him before the hugger does. Meanwhile, Mulder is distracted from the case with the sudden reappearance of his sister Samantha.
The alien bounty hunter kidnaps Scully and wants to trade her for Mulder's sister, who is revealed to be a clone herself. After the trade goes badly and Mulder discovers the truth about Samantha, he tracks the bounty hunter to his ship buried in the arctic ice and demands the whereabouts of his real sister.
The death of a federal construction worker and the destruction of various properties can only be tied to an escaped elephant. Yet, no witnesses claim to have seen the animal.
The crews of a Navy ship, who have abandoned their boat in a life raft, were rescued 18 hours later. But all of these sailors appear to have aged many decades in the course of days. Mulder suggests that the ship is caught in a time field which is speeding up their aging.
Mulder and Scully travel to Gibsonton, Florida, a town built and populated by circus and sideshow performers to investigate the death of Jerald Glazebrook, The Alligator Man. While searching for leads on the hugger, the agents come across many bizarre characters including the local sheriff who was once known as Jim Jim, the Dog-Faced Boy.
Mulder and Scully investigate the death of a young boy who Mulder believes was lured to his death by an unseen force while the boy's Romanian grandmother claims the child was evil.
When a package sent to a convict at a prison facility unleashes a deadly sickness that kills a dozen men, Scully is called in to investigate the quarantined area, while Mulder tracks two escapees who may be carrying and unknowingly spreading the disease.
Mulder and Scully investigate on a case where a residue was all that was left of a victim's body. Their investigation takes them to a chemical testing plant where a physics doctor who was involved in a freak accident, has now turns his shadow into a deadly weapon.
An FDA inspector has been reported missing and the case is given to Mulder and Scully. Scully feels that the FBI hierarchy is giving them an assignment unrelated to the X-Files, but Mulder believes that there is more to the case. Venturing to Arkansas, where the FDA inspector was reviewing the conditions at a chicken processing plant, the partners find evidence of foul play.
When Mulder obtains what could be the original and uncut MJ documents containing information about the government's knowledge of extraterrestrial life; his shadowy enemies step up their harassment of him, eventually leading to his apparent hug.