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.
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.
The reappearance of Cassandra Spender and the return of the faceless alien rebels threatens to expose The Syndicate. Cigarette Smoking Man reveals all about the alien conspiracy to a new protege he trusts to help his work continue.
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.
A woman desperately attempts to change the outcome of the events of a day she is forced to relive again and again in which her boyfriend explodes a bomb during a failed bank robbery killing everyone inside, including Mulder and Scully.
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.
While infiltrating a defense contractor conference in Las Vegas, The Lone Gunmen are reunited with Susanne Modeski, the mysterious woman who disappeared 10 years earlier after the trio first came together to help her.
The skeletal remains of a young couple are found after they have been missing for only three days in an area known for UFO activity. Mulder and Scully have different experiences in the investigation but nothing is quite as it seems.
Mulder believes metallic objects discovered on the coast of West Africa are proof of the extraterrestrial origin of life on Earth. He falls mentally ill under the apparent influence of the artifact while Scully goes to Africa for answers.