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.
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.
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.
"How the Ghosts Stole Christmas"
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.
"Terms of Endearment"
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.
"The Rain King"
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.
With the X-Files reopened, Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) 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 (Chris Owens) and Diana Fowley (Mimi Rogers) taking over instead.
With Mulder trapped in a car by a seemingly deranged man (Bryan Cranston), 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.
The unexplained death of a young handicapped girl prompts Father McCue to ask Scully for her help, but her investigation leads her to a mystery she's afraid to understand.
"The Pine Bluff Variant"
Scully begins to grow suspicious of Mulder, whose increasingly strange behavior suggests he may be serving another agenda. Guest starring Daniel von Bargen and Sam Anderson.
"Folie à Deux"
Mulder and Scully encounter a delusional man who believes his boss may be a monster – and is willing to pay any price to prove it.
Investigating the murder of a chess player, Mulder and Scully meet a boy who may be the embodiment of everything in the X-Files. This episode marks the first appearance of Diana Fowley (Mimi Rogers)