Six years after the events of the series finale, Mulder lives in seclusion following his murder conviction, and Scully has taken a job as a physician at a Catholic hospital. It doesn't take long before the FBI comes knocking, requesting Scully's help in locating her former partner. The offer is this: if Mulder assists in a difficult ongoing investigation, the charges against him will be dropped.
Helping the two veterans on the case is young agent Dakota Whitney, and a former priest named Joseph Fitzgerald Crissman. Crissman was defrocked by the church after being found guilty of multiple counts of child molestation. Despite his past, Joseph is brought in to assist via his purported psychic powers. The investigation leads to many strange and unexpected places, with death lurking around every corner. Will Mulder and Scully live to solve their next X-File?
Doggett and Reyes investigate the death of an EPA official. Scully who has returned to her teaching position at the FBI Academy in Quantico was asked to help out. Doggett and Reyes might have found the woman who possesses knowledge of a possible government cover-up involving Scully's baby.
Doggett has found Shannon McMahon who killed the EPA official. She claims to be a super solider. Meanwhile, Scully's baby is showing signs of being extraordinary.
Doggett and Reyes investigate a double homicide that has all the signs of a satanic ritual killing. While Doggett is convinced that a doctor is orchestrating the crimes from within the hospital, Reyes believes it points to the existence of an evil entity.
Doggett is clinging to life in the hospital following a shooting and Reyes has been accused of attempted murder after a witness identifies her as the shooter.
Doggett and Reyes asked Scully to help them to investigate the bizarre death of a teenager who died while performing a stunt for a cable TV show.
Scully has to decide whether she should put Mulder's life in danger by looking for him after a couple claims that their baby has the same abilities as William and they will only talk to Mulder about the information they have revolving around the super soldier program.
An amnesic Doggett is wandering in a small Mexican town. Meanwhile, Scully and Reyes went searching for him.
Doggett and Reyes investigate a series of murders where the victims were skinned alive. Scully was called in to help out and they found the murders to be linked to a case from 1960.
Scully decides to take drastic measures to protect William when she suspects that he may have more special abilities than she knew.
Scully desperately wants to rescue William from his kidnappers, so she enlists the help from the Lone Gunmen.
Reyes is in a coma after a car accident. Scully and Doggett desperately search for a way to help her while Reyes found herself in a strange place.
Scully, Doggett and Reyes have to reopen one of Doggett's old cases to determine whether the man dubbed as The Screwdriver Killer and has recently been released from prison was really guilty or not.
Using numerology, Reyes managed to deduce that a single killer is behind a series of murders. Reyes and Scully also discover some clues left by a mysterious stranger.
Agent Leyla Harrison asks Doggett and Reyes to investigate the death of a woman who was presumed to have stabbed herself repeatedly. Harrson suspects a man who can control terrifying creatures is behind the murder.
Scully, Doggett and Reyes ask for the help of the Lone Gunmen when Morris Fletcher gives them information about the Super Soldiers.
A severely deformed man is captured in the X-Files office while trying to steal documents about Mulder's sister. Doggett and Scully becomes suspicious of his real identity when his DNA is found to match that of Mulder.
An FBI profiler links a series of murders to the killing of Doggett's son. However, soon Doggett and Reyes start to wonder about his involvement in the murders.
The agents are investigating a mysterious death outside the house which the original Brady Bunch series was filmed. There, they meet a man who is obsessed with The Brady Bunch.
Mulder is on trial before a military tribunal that seeks to justify and prove the existence of an alien conspiracy and The X-Files.
Although several witnesses testified to help Mulder, he was found guilty by the military panel and sentenced to death by lethal injection.