Mulder is less than thrilled when an Office of Professional Conduct board refuses to reassign him and Scully to The X-Files and even more so when he learns that Agent Spender and Agent Fowley have become their successors. When Gibson Praise reappears and comes to them for help, Mulder and Scully attempt to continue their quest undercover despite having fewer friends and less access and protection than ever before.
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.
Mulder goes to the Bermuda Triangle when he learns that the Queen Anne, a British luxury liner which disappeared during WWII, has reappeared in the middle of the Sargasso Sea. Mulder's boat is wrecked and after floating in the water, he is hauled aboard the ship which has just been hijacked by the Nazis searching for the man who will build the atom bomb.
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.
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.
After a scan of a couple's unborn child is found to have strange growths protruding from the head and back, the fetus is taken from inside the mother by a demon creature while she is asleep. Mulder heads to investigate after Agent Spender dismisses the claims, and discovers that the father is actually a demon who wants to have a normal child.
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.
Mulder and Scully have 24 hours to save A.D. Skinner from being killed by a biologically engineered disease. The disease appears to be created by a shadowy government organization, but in order to save Skinner's life they must determine who wants him dead and why. With Skinner's condition worsening, Mulder seeks assistance from Senator Matheson, who he hopes can provide some answers and help him to find a cure.
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 Cigarette-Smoking Man recites to an unseen listener everything about the work of the Syndicate involving a global conspiracy in cooperation with an alien species, Cassandra Spender reappears and is pursued by the scientists who would rather hug her than keep her alive. Cassandra runs to Mulder's apartment and demands that he shoot her because she is the culmination of 50 years work - a living alien/human hybrid - and colonization will begin if the aliens find out about her.
The Cigarette-Smoking Man reveals all the government secrets from the past 50 years in order for his son, Jeffery Spender, to join him in his work. Mulder learns that the final stage of the conspiracy will soon begin with the hybridization of the Syndicate members, and he must stop it from happening. Agent Spender deceives his father and arranges for Mulder and Scully to be reassigned to the X-Files, which doesn't sit too well with the Cigarette-Smoking Man.
Arthur Dales summons Mulder and Scully to his holiday home in Florida where he is concerned over the disappearance of his neighbors. Despite the raging hurricane, Mulder and Scully head out to investigate and discover several strange deaths caused by an octopus-like sea creature that swam in through the overflowing sewer system.
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.
On their first official case back on the X-Files, Mulder and Scully go undercover as a married couple at a prestigious planned community where several residents have recently disappeared after failing to comply with the rules and regulations.
A mysterious dog thought to be the last of a rare Asian breed is responsible for several murders which Mulder and Scully are investigating. Now the agents have to find a way to stop the dog before it kills again.
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.
A writer living next to Mulder becomes obsessed with Scully and confesses to her that he is using her for a character in his novel. Scully finds herself strangely drawn to him even though he is now the prime suspect in the hug case that she and Mulder are investigating.
Mulder meets with Agent Arthur Dales' brother (also named Arthur) and is told a tale of a talented negro baseball player from Roswell, New Mexico in the 1940's who may have been an alien that ran away from his colony because of his love for the game.
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.
Two scientists confer about each of their metal objects that were found in Africa and they theorize that the objects are pieces of a puzzle which could be undeniable proof that human, plant, and animal life did not originate on this planet. When one of the scientists is killed and the objects are stolen, the agents investigate and Mulder begins to experience severe neurological pain caused by the objects.