Mulder and Scully's ability to pursue the X-Files and their partnership is threatened by the hunt for a deadly creature in the Arizona desert, whose capture could prove Mulder's theories about the existence of extraterrestrial life.
An anonymous tip finally brings Mulder and Scully to the mecca of all UFO lore, Area 51. But when the agents witness the flight of a mysterious craft, their lives are profoundly and perhaps irrevocably altered.
On Christmas Eve, Mulder and Scully stakeout a house that is supposedly haunted by the ghosts of two lovers who killed each other in a lovers' pact 81 years before. Inside, the agents find two apparitions who are more than willing to give insight into the relationship and personalities of Mulder and Scully.
Mulder suspects demon fetal harvesting when a woman claims her unborn child had a horn and tail and was taken by a devil while she slept. While others conclude that the woman killed her own baby, Mulder suspects that her husband is involved and that he may be the devil in disguise.
A mayor of a small town asks Mulder and Scully to investigate Daryl Mootz, a man who apparently can make it rain at will. The mayor believes Mootz is responsible for causing a local drought so that he can charge individuals for rain on their farms.
Skinner comes down with a mysterious condition that puts him on the verge of death. An unknown voice on the phone tells Skinner that he has 24 hours to live. Mulder and Scully rush to find a cure for his condition. His impending death is somehow linked to S.R. 819, a Senate resolution that will supply money and medical supplies to the World Health Organization.
Agent Scully gets paired up with a new partner to investigate a singular case. Alfred Fellig, a freelance crime photographer, has a knack for arriving at crime scenes shortly after the murder and long before the police arrive. Local authorities suspect Fellig may be killing the victims himself before photographing them.
After being gone for almost a year following her abduction, Cassandra Spender reappears, in perfect physical condition as the first successful alien/human hybrid. The consortium scrambles as the faceless alien rebels seek to expose their conspiracy with the colonizing aliens. Mulder and Scully try to discover the identity of the Cigarette Smoking Man and protect Cassandra from the consortium who want her dead.
Agents Mulder and Scully find themselves under strict quarantine after coming into contact with Cassandra Spender. Meanwhile, the suspicious Diana Fowley increases her loyalties to the Cigarette Smoking Man.
At Arthur Dales' request, the agents go to Florida during a hurricane to investigate the disappearance of Mr. Dales' neighbors, two marine biologists and their son. During the storm, Mulder and Scully get stranded in an apartment building where a sea monster is on the loose.
A bank robbery gone wrong turns into disaster for Mulder and Scully. Mulder gets shot by the bank robber, and he and Scully, along with everyone else in the bank are blown up by a bomb strapped to the bank robber's chest. However, this same day continues to repeat in an endless cycle always ending in the same result.
An escaped convict apparently has the ability to pass through solid objects. He has $90,000 hidden somewhere from the bank robbery for which he was imprisoned. Mulder and Scully must find the deadly convict before he can get to his ex-girlfriend and the money.
An introverted writer, Philip Padgett, develops an obsession with Scully and moves into Mulder's building in order to be closer to her. Inspired by her, Padgett writes his magnum opus: a story of secret love and serial murder, featuring Scully and Padgett as main characters. However, the murders in his story begin occurring exactly as written. As he struggles to finish his novel, Padgett realizes that only Scully's death can produce the perfect ending.
Mulder uncovers a story involving a Negro baseball player in the 1940s who played for a minor league team in Roswell. When in a photograph he sees the Alien Bounty Hunter it is assumed that Josh Exley, the baseball player in question, might just be alien himself.
The Lone Gunmen are at a defense contractors convention in Las Vegas trying to get inside information on military secrets. When Byers spots Susanne Modeski at a casino, he convinces the other lone gunmen to trick Scully into coming to Las Vegas to help them investigate why Susanne Modeski is there and what she is up to.
A young married couple's skeletons are found together on a field in the mountains after only being reported missing for three days. The area where their skeletons were found is known for UFO activity, so Mulder and Scully go there to investigate it. Mulder finds the couple alive and all signs point to an alien abduction. But everything is not as it seems.
An artifact with strange engravings on it is found off of the coast of Africa. When a rubbing of these engravings is shown to Mulder, confusing noises happen inside his head. The agents look to uncover the origin of this mysterious artifact and to find out why it is having a singular effect on Mulder.