X-Files Season Two

Little Green Men
With the X-Files shut down, Mulder is assigned to wire taps while Scully returns to teaching at Quantico. All hopes dulled of ever finding evidence to what he has seen, Mulder is about to give up hope; luckily, however, the proof he was looking for may have just presented itself. With the X-Files closed, Scully has been assigned as an instructor at the FBI Academy while Mulder is doing menial surveillance work. After meeting with Senator Matheson, one of his supporters in regards to The X-Files, Mulder disobeys orders and heads to an abandoned SETI site in Puerto Rico which has unexplainably reactivated itself and could provide proof of contact with extra-terrestrial life.
The Host
A body is found in the sewers of New Jersey, and Agent Mulder is strangely assigned to the case. Soon, the killer seems more like an X-File-worthy creature than a homicidal man. Could his placement in this case be coincidence, or does somebody want the X-Files to continue? AD Skinner sends Mulder to investigate a body which washed into the New Jersey sewer from the ocean. Mulder believes that the basic blue-collar assignment is punishment, but on Skinner's own admission what he discovers is a true X-File.
Blood
A small county in Franklin, Pennsylvania has been home to a series of mass killings, where the murderer seems to have gone crazy in an unexplainable way. Mulder, with the help of Scully and his old buddies at The Lone Gunmen, tries to solve the case before it happens again. When several violent deaths in a small farming community are connected by the destruction of digital devices, Mulder believes that people are being driven to kill by the use of subliminal messages in the digital readouts.

Sleepless
A doctor specializing in sleep deprivation is found dead in his condo after reporting a massive fire outside the door. No fire was seen nor reported otherwise, but when Mulder asks Scully to take a closer look, she finds disturbing evidence that questions reality. Mulder reluctantly accepts a new partner, Agent Alex Krycek, and requests a strange case because someone put an audio tape in his morning paper. When his request is granted they investigate the deaths of several Green Beret soldiers who participated in a sleep deprivation experiment during the Vietnam war. But before long it becomes clear that not one of these men have slept in over 20 years...
Duane Barry
An institutionalized man who claims to have had multiple alien encounters escapes the hospital, taking his doctor with him. Agent Mulder is brought in to help the hostage negotiations. All the FBI wants is the hostages out alive, but all he wants is to be heard... Mulder is called to a hostage situation involving Duane Barry, a former FBI Agent who claims to be an alien abductee and wants to get back to the abduction site with someone who will be taken instead of him. Unfortunately, the someone he eventually chooses is Scully.
Ascension
Reviewing Scully's message to him from before she was taken, Mulder tries to piece together where Duane Barry is headed. Krycek, though reluctant, agrees to help and tags along. There are forces at work all around them; some are military, some may be small and gray. When Mulder finds out that Scully was kidnapped by Duane Barry, he risks the wrath of his superiors and the annoyance of Agent Krycek in order to do whatever it takes to find her. Meanwhile, Krycek is found to be reporting Mulder's activities to the CSM.
3
Whilst Agent Scully is still missing, Agent Mulder embarks upon an investigation involving vampires in Los Angeles, subsequently becoming involved with a sultry female vampire who yearns to escape her lifestyle. Truely alone for the first time since Scully found her way to the basement of the J. Edger Hoover Building, Mulder throws himself into his work, and into the bizarre world of vampire-fetishist in search of a trio of serial killers. But Mulder finds himself falling for the one woman that may be the prime suspect

One Breath
An unconscious Scully appears in the Emergency Ward of NE Georgetown Medical Center. As her mother and sister look after her, Mulder vows to track her captors down. After a talk with Asst. Director Skinner, Mulder hunts down the Smoking Man and demands the truth - at any cost. Scully mysteriously appears in a Washington hospital, alive but in a coma, and Mulder must fight to keep her alive in order to find out what happened to her and who did it to her. Meanwhile, Scully fights her own personal battle as she decides whether to stay or go on to the next world.
Firewalker
A distress signal is received from a volcano research team in the Cascades. The last captured image from their robot, Firewalker, shows a dead team member and something else inside the volcano. Mulder and Scully investigate, unaware of the true nature of the killer.
Red Museum
Agents Mulder and Scully investigate when a religious cult is accused of kidnapping, branding their victims with the words 'He is One', or 'She is One'. While investigating the connection between the abduction of several teenagers and a rural religious cult, Mulder & Scully discover a secret test being performed on the children using the "Purity Control" alien DNA from 'The Erlenmeyer Flask' which leads Mulder to the Crew-Cut Man, Deep Throat's murderer.
Excelsis Dei
A nurse (Teryl Rothery) who works in a home for the elderly in Massachusetts claims to have been raped by an invisible assailant. Mulder and Scully investigate, and soon find that the patients of the home are not quite what they seem. One of them appears to be seeing what isn't there, and the continued occurrence of seemingly inexplicable events (including apparent miracle cures for Alzheimer's Disease) point toward an extraordinary explanation.

Aubrey
Several murders in Aubrey, Missouri which occurred in the 1940's resurface when a county police officer digs up the bones of the missing FBI agent once assigned to the case. A similar murder occurred just a few nights ago, and it is up to Mulder and Scully to bring the story to rest.
Irresistible
Bodies are being dug up in Minneapolis, Minnesota, nails and hair removed from the young female victims. Mulder creates a working profile of the suspect, though the case is hard for Scully to accept. The killer is starting to kill to retrieve, and she may be next.
Die Hand die verletzt
A group of teenagers in New Hampshire, who decide to test an old myth about satanic rituals, nearly escape a killing which leaves one of them dead. Mulder and Scully investigate the case, which leads them to suspect the town, the school, and, most importantly, its staff.
Fresh Bones
When a soldier stationed at a processing center for Haitian citizens crashes his car into a tree marked by voodoo, his wife refuses to believe it was suicide. Mulder and Scully search for the man responsible, but must be careful that they don't get marked next.
Colony
Upon receiving three obituaries of three identical-looking men via anonymous e-mail, Mulder and Scully investigate the growing number of homicides throughout New England. When a new charade of evidence is presented, neither Mulder nor Scully know what to think.

End Game
The search for the bodies of those in the lake continues, as a note from Mulder's father leads him to an abortion clinic in Rockville, Maryland. What he finds he can neither believe nor explain, but the doctors there need his help, before they are exterminated.
Fearful Symmetry
An elephant found roaming an interstate road in Boise, Idaho escaped from a locked cage in a zoo across the county. The night before, a construction worker was mauled by a seemingly invisible force. Many other forces are at work, and Mulder and Scully must see them all.
Død Kalm
When some people on a ship are rescued, it is discovered that they are aging and later, dying. Mulder takes it upon himself to investigate the ship, which he believes has been the target of Philadelphia Experiments.
Humbug
The strange death of a circus sideshow attraction in Gibsonton, Florida, leads Mulder and Scully on a bizarre whodunit adventure into the world of the performing arts. Was the killer the Fiji Mermaid, the Dog-Faced Boy, or any of the town's other inhabitants?
The Calusari
A two-year-old boy in a Virginia park is mysteriously killed, and a further look shows a ghostly figure luring him. Mulder and Scully investigate despite an existing official inquiry, and learn that the boy's brother is in great danger as well - for evil follows evil.
F. Emasculata
When a package with infected contents releases the virus on its inmate recipient, a dozen prisoners contract it and Mulder and Scully are mysteriously called in to help. What they find demands that the truth be told to the public, but that's the one thing they cannot do.
Soft Light
Three deaths have occurred around Richmond, Virginia. The only traces which each of the victims seem to have left behind are black scorch marks of unknown origin. Mulder and Scully are called in by an old student of hers, and the search for the truth begins in its shadows.
Our Town
Reports of foxfire on a field in Dudley, Arkansas lead Mulder and Scully to a bizarre situation regarding the townsfolk. Employees of the Chaco Chicken Corporation are displaying bizarre behavior, and the death rate is slowly increasing.
Anasazi
A man known as "The Thinker" has hacked into the U.S. Department of Defense mainframe and uncovered 50-years-worth of proof that the Gov't has been dealing with aliens. Mulder and Scully race against time to distinguish truth from lies, uncover the secrets, and survive them.