Scully and a colleague try to decipher the symbols on the spaceship beached in Africa before their rival can take over the dig, but the ship starts recreating the Plagues of Egypt. Skinner and Kritschgau test Mulder's telepathic ability.
Scully searches for Mulder after the Cigarette Smoking Man takes him from the hospital for unknown purposes. An unconscious Mulder dreams of a better life away from his mission and the X-Files. But perhaps he is being led astray.
At the turn of the 21st century, a religious fanatic enlisted by the Millennium Group resurrects four members of the group as zombies to bring about the end of the world. Mulder and Scully enlist the help of Frank Black to help stop the apocalyptic designs of the Millennium Group.
A man is tossed off the top of a 29 story building by gangsters. Amazingly, he gets up and walks away unscathed. Mulder and Scully investigate when Mulder suspects this man may have paranormal abilities. The man in question may just be the luckiest man on Earth.
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.