After the events of The X Files (1998) movie, Mulder and Scully's new boss, Kersh, assigns agents Spender and Fowley to work on the X-Files instead of them. Ignoring this, Mulder takes Scully on a hunt for a rampaging alien.
A man tormented by a piercing sound that could make his head explode unless he heads west as fast as possible takes Mulder hostage to drive for him, while Scully rushes to find the cause of this affliction that also killed the man's wife.
Mulder boards the wreck of a legendary missing WWII ship that suddenly appeared in the Bermuda Triangle. The ship turns out to be a time portal. Now Scully must use all of her wits to try and get the unwilling FBI to help her save him.
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 there, Mulder and one of the Men in Black, Fletcher, somehow switch bodies - and lives.
A pregnant woman's baby is snatched away from her belly by a devil. Agent Spender believes the case is a joke, but Mulder decides to look into it on his own anyway. His investigation focuses on the woman's husband.
A rookie agent asks for Scully's help in proving that a quaint crime scene photographer is a serial killer. With some help from a bored Mulder, Scully discovers the man's actual dark secret. And an old prophecy regarding Scully comes true.
The alien rebels return to kill abductees including Scully and Cassandra Spender. With the Syndicate in shambles, the Cigarette Smoking Man reveals the truth to Agent Spender hoping that he will continue his work.
Everyone prepares in their own way for the alien rebels' bloody endgame after which nothing will ever be the same again. Mulder and Scully try their best to stop the bloodshed and save Spender's mother.
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.
A series of murders is blamed on a mythical Asian dog that supposedly escaped from the US cryptozoologist who caught it. Mulder asks a reclusive female dog expert for help which angers Scully. The woman leaves him a special gift.
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.
A strange writer infatuated with Scully moves in next door to Mulder and proceeds to slowly bewitch her through his writing. Mulder investigates the man and realizes that he may be behind a series of killings involving psychic surgery.
Searching through an FBI reference book, Mulder finds a photograph of Arthur Dales with a baseball team and the alien bounty hunter. Mulder goes to Arthur Dales' house to ask him about the photograph. There he finds Arthur Dales' brother, also named Arthur. Mr. Dales proceeds to tell Mulder a story of a 1940s Negro baseball player in Roswell named Josh Exley who was closing in on breaking some professional baseball records. Mr. Dales tells how he was assigned to protect this player from the KKK and that Exley was actually an alien.
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.