This season was the first to be filmed in Los Angeles, California, after production was moved from Vancouver, Canada. With the X-Files reopened, Fox Mulder and Dana Scully eagerly hunt for a deadly creature in the Arizona desert. What they find seems to support Mulder’s revived belief in aliens, but is discredited when the agents are not reassigned to the X-Files, with Jeffrey Spender and Diana Fowley taking over instead. With Mulder trapped in a car by a seemingly deranged man, Scully races to determine if the man is suffering from a deadly illness—and if Mulder is in danger of becoming the next victim of a government virus. Mulder goes in search of a ship that disappeared in the Bermuda Triangle in 1939. But when he gets on board, Mulder finds that he—and all the passengers and crew (as well as some strangely familiar ones)—are still stuck in the past. 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.
Scully begins to suspect that her partner’s strange behavior is more than it appears to be, while Mulder fights to return his life to normal before it’s too late. On Christmas Eve, Mulder convinces Scully to put aside her gift wrapping and stake out a reputed haunted house. But they discover a pair of lovelorn spectres living inside the house who are determined to prove how lonely the holidays can be. When a mother is accused of killing her unborn child, Mulder and Scully discover that the father has his own secrets, and he’s not the only one. In a small town plagued by drought, Mulder and Scully come upon a man who claims to be able to control the weather—at a hefty profit. Yet the agents discover a force of nature at work even more powerful than the weather, and just as unpredictable. Assistant Director Walter Skinner (Mitch Pileggi) is poisoned. Mulder and Scully have 24 hours to save him, but in order to do so, they must determine who wants him dead, and why. Scully learns that she, but not Mulder, is being given a chance to prove her worth at the FBI, and—paired with a new partner—she investigates a crime scene photographer with an uncanny knack for arriving just in time to see his victims’ final moments. What she does not expect is for Death to play a role himself. When Cassandra Spender (Veronica Cartwright) is returned, Mulder, Scully and Agent Spender find themselves facing the exposure of the conspiracy involving extraterrestrials; while the worried Syndicate take evasive measures.
While Cassandra reveals the truth about the alien conspiracy to Mulder, her ex-husband—The Smoking Man—does the same to Agent Spender in an effort to convince him to work with the conspiracy. Mulder and Scully are looking forward to cases again. Instead, Arthur Dales, now living in a Florida trailer park, calls the agents for help when a neighbouring family disappears; and, with a hurricane approaching, Mulder and Scully find themselves trapped with a group of residents in a building where there is something in the water. The world is trapped in a time loop, and only one woman seems to know. Each day the events that happen differ slightly; “free will”, as Mulder calls it. A bank robbery is committed over and over again until they can stop the eventual bombing of the place from occurring. Several disappearances at an idyllic planned community lead Mulder and Scully to go undercover as a married couple. However, they soon discover that the president of the homeowners’ association takes the community covenants and regulations more seriously than they could have imagined. An Asian dog, called the Wanshang Dhole, thought to be extinct is blamed for several killings. Mulder and Scully join an obstinate Sheriff, a seemingly eccentric hunter, and a reclusive canine expert to find it. However, there is more mystery to the expert than meets the eye. After a prison camp is destroyed by a tornado, an escaped inmate is suspected of killing the warden. As the inmate hunts down his old girlfriend, he finds out where his child is and attempts to take him back. Mulder and Scully set out to find him and discover that he has the ability to pass through conductive materials. A series of murders takes place where the heart has been removed from the victims. A writer that lives next door to Mulder is writing a novel about the murders before they actually happen. Scully finds herself confused and drawn to the writer, who has a romantic interest in her.
While working in Roswell, New Mexico in 1947, young cop Arthur Dales (the brother of the Arthur Dales who started the X-Files) stumbles across a “negro” baseball player who is actually an alien with a love of the game hiding among humans. While at a conference in Las Vegas, The Lone Gunmen run into the enigmatic Susanne Modeski. After deceiving Scully into joining them, the trio soon find out that Susan’s fiancé is planning to use her new brainwashing drug for political assassinations. The skeletonized remains of a young couple are found in the fields of North Carolina. When Mulder and Scully go to investigate, they find that a giant fungal life form releases an LSD-like drug into the air with spores, and then slowly digests its victims. Mulder and Scully fall into its trap and are not sure of what is reality and what is fantasy. Mulder believes that metallic objects discovered in Africa are proof that life originated elsewhere in the universe. Skinner, now in contact with Alex Krycek and Agent Fowley, begins monitoring Mulder and Scully on the case. Mulder, due to the apparent influence of the artifact, falls mentally ill, which leads to Scully travelling to Africa alone.