2.1 "Little Green Men"
Long after the shutdown of the X-Files division, Mulder finds his own belief in the truth waning. So when an old friend gives him a new reason to believe, he goes alone to an abandoned SETI program site in Puerto Rico. Concerned, Scully tries to contact him before someone else does.
2.2 "The Host"
A man's decomposed body is found in the sewers of Newark, NJ and Mulder is given this supposedly routine murder case. But after Scully's autopsy turns up a parasite living inside the body and a sewer worker is attacked and bitten by something, it opens up a whole new can of worms.
A recent rash of killings in the small town of Franklin, PA brings Mulder to profile the murderers. A task made more difficult by the fact that none of them had any previous history of violence and all died at the end of their berserker rages. The only clues he has is some destroyed electronics and an unknown organic substance.
An audio cassette hidden in his morning paper brings Mulder to request the case of a scientist's death consistent with burning, despite the lack of any evidence of any flames or burns. He is given his request...along with a new partner. But together they must find the murderer before the case can be laid to rest.
2.5 "Duane Barry"
An ex-FBI agent escapes from a mental hospital and holds several people hostage in a travel agency. Mulder and Krycek are sent in to help with the negotiations since the man claims to have been a UFO abductee. Part one of two.
Returning home to find the phone message left by Scully, Mulder immediately sets off to locate Duane Barry, but is unable to make any headway until a police video from a traffic violation yields a clue which lifts his spirits. Part two of two.
Despite Scully's absence, Mulder finds the strength to continue his work on the recently reopened X-Files. When he recognizes a Los Angeles killing as the work of the Trinity murderers, a trio of killers with a fetish for drinking blood, it gives him work in which to immerse himself.
2.8 "One Breath"
Scully mysteriously appears in a Washington D.C. hospital, kept alive almost entirely by machines. Frustrated by his inability to help her, Mulder drives himself crazy trying to find the people responsible. Though his quest for vengeance could make him exactly like those whom he despises.
A malfunction in a robot designed for volcanic exploration yields evidence of a lifeform living in the caves. When this lifeform seemingly causes the death of a member of the research team, Mulder and Scully are flown out to the site to investigate before anyone else dies.
2.10 "Red Museum"
Several Wisconsin teens are found wandering outside in their underwear with "He is one" scrawled on their backs. Mulder and Scully travel to investigate this aberrant behavior, though the strangest thing in this meat-producing area is a cult of vegetarian "walk-ins."
2.11 "Excelsius Dei"
Mulder and Scully's latest case begins with the rape and battery of a nurse in a Massachusetts convalescent home. What makes it an X-File is her claim that her attacker was invisible. But upon their arrival, they discover that the unrest is not limited only to the live-in residents.
In a dream, a policewoman experiences the memory of a serial killing and unearths the body of the FBI agent sent to investigate it nearly 50 years ago. When the serial killer strikes again, Mulder and Scully work with the detective to determine the killer's identity.
A female corpse, dug-up and mutilated, is brought to Mulder's attention by a Minnesota agent claiming it as the work of aliens. Mulder believes otherwise and is vindicated when a similarly mutilated prostitute is found. Meanwhile Scully has to deal with how this case seems to be affecting her.
2.14 "Die Hand Die Verletzt"
Some teenagers' feign an occult ritual in an attempt to score and inadvertantly cause the murder of one of their group. When Mulder and Scully are called to look into the matter, the town's real worshippers attempt to hide their tracks though they fear that the boys' attempt to "get some," got them more than they thought.
2.15 "Fresh Bones"
When a soldiers stationed at a resettlement camp for Haitians drives himself into a tree, Mulder and Scully are called by the grieving and fearful wife. Her fears of a voodoo curse seem only to be reinforced by the beliefs and actions of many of the local residents, including a few of the other soldiers.
A newspaper ad placed to locate a certain doctor sets off the murder of several people with the same face. When Scully and Mulder locate another look-alike, they work to find him before the killer does. Coming to Mulder's aid is another familiar face, but one he wasn't expecting. Part one of two.
2.17 "End Game"
When Scully is taken captive by the bounty hunter, Mulder must give up a recently returned loved one in exchange. However, when his trap goes awry, Mulder tracks the hunter far to the icy north in an effort to find the one he has lost twice. Part two of two.
2.18 "Fearful Symmetry"
The death of a federal construction worker and the destruction of various property can only be tied to an escaped elephant. Yet the witnesses claim to have seen no animals which might have caused the turmoil. So, Mulder and Scully check out the local zoo whose claim to fame is that they've never had a successful animal birth.
2.19 "Dod Kalm"
The last known position of the U.S.S. Argent was in the Norwegian equivalent of the Bermuda Triangle until a boatload of survivors is found. What particularly catches Mulder's inquisitive eye is that all of these sailors appear to have aged many decades in the course of days.
Mulder and Scully must find the paranormal among the abnormal when they are sent to investigate a long standing series of ritualistic killings which match no known patterns. The latest of which was the death of the "alligator man," just one of many sideshow acts around which the town of Gibsontown, FA is built.
2.21 "The Calusari"
A photograph taken just prior to the death of a two year old boy yields evidence of some supernatural intervention which piques Mulder's curiosity. When another death in the family occurs, the grandmother of the remaining child requests the aid of some Romanian ritualists in order to cleanse the home of evil.
2.22 "F. Emasculata"
Mulder and Scully find themselves sent to a penitentiary in order to participate in the retrieval of two escaped convicts. Confused as about the reason for FBI involvement, they look a little deeper and discover an highly contagious and deadly disease has infected many of the inmates, and possibly the two escapees as well.
2.23 "Soft Light"
An ex-student of Scully's asks Mulder and Scully to help her with her first investigation concerning a number of disappearances with very few clues. Mulder ponders the idea of spontaneous human combustion but rethinks it when they find a man who is afraid of his own shadow.
2.24 "Our Town"
Dudley, Arkansas is the site of the latest investigation for Mulder and Scully, who are sent to find a missing poultry inspector. The case takes a twist when another poultry worker is shot after she goes insane, giving Mulder a hunch that the townfolk really are what they eat.
2.A "The Secrets of the X-Files"
This was a one hour special retrospective on the last two seasons of the show.
The trust that Mulder and Scully is sorely tested when Mulder begins acting strangely. His aberrant behavior is compounded when the Lone Gunmen direct him to a hacker who managed to break into some very closely guarded files. So, the Smoking Man quickly takes action while Scully investigates Mulder's abnormal behavior. Part one of two.