An accident at Rousch Technologies brings an E.B.E. to term inside a human host. Killing one person, the creature is now on the loose in Phoenix. Meanwhile, Mulder and Scully try to support their work on the X-Files, but their arguments fall on deaf ears. Skinner, behind the back of the OPR committee reviewing the agents' work, gives Mulder information on the death of the human host.

While working on a domestic terrorism assignment, Mulder comes across an apparant hostage situation turned high-speed chase in Northern Nevada that seemingly defies belief: A woman's head explodes in a police car, yet there is no indication she was shot. Defying orders not to pursue cases resembling X-Files, Mulder and Scully head to Elko, Nevada, to assist the local police.

With the rain falling at sea, Mulder is pulled aboard HMS Queen Anne, long thought to have disappeared in the Bermuda Triangle. However, the crew that pulls him up are from the year that the ship had disappeared: 1939. While Mulder tries to figure out what to do, the Lone Gunmen approach Scully while at work and ask her for help in finding Mulder.

An anonymous tip brings Mulder and Scully to Groom Lake, Nevada; better known as Area 51. When they witness the flight of a mysterious craft, Mulder mysteriously swaps bodies with an Area 51 Man in Black.

Scully finally realizes that real Mulder is still in Nevada and rushes there to help him, while Mulder fights to return his life to normal before it's too late.

On Christmas Eve, Mulder has Scully meet him at a supposedly haunted mansion in Maryland. Scully, however, doesn't have time for ghost stories and begins to leave when she sees Mulder leave his car and approach the house. Upon entering the manse, both discover a pair of star-crossed lovers who died ages ago. On this night, the two ghosts are going to have a bit of fun with their guests.

Mulder and Scully investigate a case where a mother is accused of killing her unborn child. However, they begin to suspect a more sinister force at work.

Mulder and Scully journey to a small town that is plagued by drought. The town's mayor, who has invited them, tells the agents that the blight is caused by a local man who, he claims, does rain dances for money.

Skinner falls seriously ill after being infected with a biologically engineered disease by a shadowy government organization. Now, Mulder and Scully have to track down the leader of the group to save Skinner.

Scully is temporarily assigned a new partner and heads to New York City to investigate a crime scene photographer who may actually be the killer. Back in Washington, Mulder continues to help his partner.

The return of Cassandra Spender, an alien abductee, threatens to finally expose the conspiracy involving extraterrestrials. The Cigarette-Smoking Man has to strike back at Mulder and Scully before they uncover the truth.

Mulder has finally found out the truth about the government conspiracy responsible for his sister's abduction, but now he doesn't know what to do with this new found knowledge.

Receiving a call from Arthur Dales, Mulder and Scully head to Florida and into a torrential downpour that is followed by a hurricane. Dales tells the two agents that he received a call from the wife of a couple he knows whose husband had been grabbed by something with tentacles.

As Mulder lies bleeding from a gunshot wound in Scully's arms, a bank robber flicks a switch that detonates a bomb, destroying a bank in Washington, D.C. Moments later, time returns to the beginning of that fateful day and the events are repeated once again.

Mulder and Scully are investigating a series of bizarre happenings in an exclusive gated community. However, they have to pose as a married couple in order to continue their investigation.

Mulder and Scully are called in to investigate a case where a mysterious dog, which is the last of an ancient Asian species, is responsible for several murders.

A convict in Mississippi is reprimanded by a dictatorial warden, who puts the convict in a solitary confinement box located outside during a huge storm in which several tornadoes touch down. When the storm subsides, the box has been destroyed, but its former occupant has escaped and wreaks havoc on those that wronged him. Mulder and Scully try to figure out his next move and how the convict is able to move through seemingly impassable barriers.

When Mulder and Scully investigate several murders where the killer leaves no clues, Scully finds herself strangely attracted to the prime suspect of the case.

Mulder and Scully find an old case involving a star player in the Negro Baseball League who has an unbelievable batting average and an incredible secret.

Attempting to gain access to intelligence conferences on new military applications, weaponry, and tactics at DefCon 99 in Las Vegas, the Lone Gunmen run into Susanne Modeski, who had been taken before their very eyes over ten years ago.

When two skeletons of a couple who have only been missing for less than a week are discovered, Mulder and Scully are called in to investigate. Soon, their investigation leads them on a journey in which nothing is quite as it seems.

An artifact found off the coast of western Africa is brought by a site researcher to be analyzed by an associate at American University. However, an interloper meets with the researcher first and kills the man, taking the artifact. The murder comes to the attention of Skinner, who hands the case over to Scully and Mulder.