Five years have passed since Scully escaped from Donnie Pfaster, an obsessed death fetishist. When Reverend Orison helps the madman escape from prison he immediately turns to the one that got away...Scully.
Mulder and Scully investigate the apparent murder of a magician who was decapitated just minutes after he was able to perform the trick of turning his head around 360 degrees. The agents are perplexed when Scully discovers during the autopsy that the deceased died well before he performed his final trick.
A man is found dead in his locked car, killed from over a hundred snake bites. However, no evidence of snakes being present is found. The man was a former member of a religious cult that believes in snake handling. Mulder and Scully believe that this snake death was no accident, and that it may have been a murder involving this snake handling cult.
The strange disappearance of a little girl leads Mulder to make connections with previous unexplained cases of missing children. Scully believes he is becoming obsessed with the case by associating it with the abduction of his sister.
Mulder and Scully are on a stakeout of a female serial-killer of prostitutes. Mulder gets called away from the stakeout by Skinner to investigate the disappearance of federal judge's daughter. The strange appearance of a raven shortly before she went missing leads Mulder to believe this case may have paranormal significance.
Scully is finishing up the autopsy of a person at a hospital. A file mix-up involving the autopsy folder and another patient's x-ray leads Scully to discover a former lover of hers has been admitted at the hospital. Meeting with him again causes Scully to re-examine the decisions she has made in her life, leading to her where she is to today.
A potential witness in a high-profile tobacco case under Skinner's supervision is found dead in his bathroom from mysterious circumstances. Skinner asks Mulder and Scully to assist him in the investigation. They find a man who smokes a unique kind of cigarettes, the second-hand smoke of which, has deadly results for the inhaler.
A screenwriter tags along with Mulder and Scully as they investigate a church bombing. The case becomes the plot of a Hollywood movie, but the agents find their case, and themselves, distorted on the big screen.
Two strikingly similar women, who do not know one another, cause people to erupt into violence upon each other, whenever these two women come in contact. Mulder and Scully set out to solve the mystery of this unexplained violence involving the two women.
Seven years after their first case, Mulder and Scully return to Bellefleur, Oregon to see Billy Miles and investigate a new series of abductions in the local forest, risking their partnership and lives.
Doggett is a little dismayed when Scully investigates a murder in a barely inhabited town in Utah without him. When Scully's car breaks down and she finds the town people aren't as sweet as they seem she struggles to find a way out of the demented town.
Doggett and Scully once again butt heads on their latest X-File which involves a boy who has returned after being missing for ten years but still appears to be seven years old, the age he was the day he was abducted.