Season | Series | Image | Title | Writer | Director | Original Airdate |
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| 25 | | ""‡ | and | September 16, |
With the X Files closed, is contacted by a political ally and sent on a dangerous mission to a radio telescope in Arecibo, Puerto Rico. Concerned for his safety, has to track down his whereabouts before someone or something else does. |
U.S. viewers (millions): million / Rating/Share: |
| 26 | | "" | September 23, |
While continuing work not related to the X-files, Mulder apparently finds evidence of a giant worm-like monster in the New Jersey sewage system. |
U.S. viewers (millions) million / Rating/Share: |
| 27 | | "" | Story by : Teleplay by : & | September 30, |
Apparently prompted by messages from digital appliances with instructions to kill, several residents of a small farming community suddenly turn violent and dangerous. |
U.S. viewers (millions): million / Rating/Share: N/A |
| 28 | | "" | October 7, |
A new partner joins Mulder as he investigates the deaths of several victims who were killed by apparently nonexistent forces. |
U.S. viewers (millions): million / Rating/Share: N/A |
| 29 | | "" | October 14, |
Mulder becomes involved in a hostage situation with an escaped psychiatric patient who claims to be terrified of frequent alien abductions. (Part 1 of 2) |
U.S. viewers (millions): million / Rating/Share: N/A |
| 30 | | "" | Paul Brown | October 21, |
Mulder attempts to search for Scully when she is abducted by Duane Barry, the escaped mental patient who recently held Mulder hostage. (Part 2 of 2) |
U.S. viewers (millions): million / Rating/Share: N/A |
| 31 | | "" | Chris Ruppenthal and & | November 4, |
With Scully missing, Mulder closes in on an "Unholy Trinity" of vampiresque killers and finds himself falling for a mysterious woman who is the prime suspect. |
U.S. viewers (millions): million / Rating/Share: N/A |
| 32 | | ""‡ | & | November 11, |
Scully miraculously appears in a Washington DC hospital, unknowingly supervised by a nurse who may never have existed. |
U.S. viewers (millions): million / Rating/Share: |
| 33 | | "" | November 18, |
When a moving shadow appears on a video transmission from a volcano, a volcanologist asks Mulder and Scully to investigate the incident. |
U.S. viewers (millions): million / Rating/Share: N/A |
| 34 | | ""‡ | Win Phelps | December 9, |
The agents investigate a suggested link between a religious cult of vegetarians and the abduction of several teenagers, although they find that the disappearances are actually connected to a deadly event in their own past. |
U.S. viewers (millions): million / Rating/Share: |
| 35 | | "" | Paul Brown | Stephen Surjik | December 16, |
Mulder and Scully uncover strange occurrences in an old-age care home when one of the nurses is attacked by an unseen force she claims to be one of the residents, a 74 year old man. |
U.S. viewers (millions): million / Rating/Share: |
| 36 | | "" | Sara Charno | January 6, |
When a detective mysteriously uncovers the remains of an FBI agent who disappeared in the s while investigating a murder case similar to a modern-day one she is investigating, Mulder and Scully believe that the original killer had passed his genetic trait of violence to his grandchild. |
U.S. viewers (millions) million / Rating/Share: |
| 37 | | "" | January 13, |
A mortuary worker who collects hair and fingernails from dead bodies begins to kill people to expand his collection, and he sets his sights on Scully. |
U.S. viewers (millions): million / Rating/Share: |
| 38 | | "" | & | January 27, |
After a teenager is ritualistically murdered in a small town, Mulder and Scully are caught up in a secret occult practice within the local PTA and a substitute teacher with odd powers. |
U.S. viewers (millions): million / Rating/Share: |
| 39 | | "" | February 3, |
After several murders occur within a Haitian refugee camp, Mulder and Scully are caught in the middle of a secret battle involving a Voodoo priest and the camp commander. |
U.S. viewers (millions): million / Rating/Share: |
| 40 | | ""‡ | Story by: & Teleplay by: | Nick Marck | February 10, |
After four identical men are killed and their obituaries are e-mailed to Mulder, a mysterious CIA agent informs him and Scully that the killer is a bounty hunter sent to destroy the start of a colony of clones. Meanwhile, Mulder is distracted when his sister, Samantha, suddenly returns. (Part 1 of 2) |
U.S. viewers (millions): million / Rating/Share: |
| 41 | | ""‡ | February 17, |
Mulder and his sister race to evade the alien bounty hunter and uncover more of the insidious conspiracy. (Part 2 of 2) |
U.S. viewers (millions): million / Rating/Share: |
| 42 | | "" | Steve DeJarnatt | James Whitmore, Jr. | February 24, |
Strange things happen in a zoo that result in several deaths, including a government employee and apparently an invisible elephant. |
U.S. viewers (millions): million / Rating/Share: |
| 43 | | "" | Story by: Teleplay by: & | March 10, |
In the North Atlantic, Mulder and Scully investigate the crew of a US Navy Ship, all of whom somehow radically aged. The agents locate the ship but, like the vessel's crew before them, Mulder and Scully also suffer from rapid aging. |
U.S. viewers (millions): million / Rating/Share: |
| 44 | | "" | March 31, |
A bizarre murder in Florida brings Mulder and Scully to a town populated by circus freaks and sideshows performers of all shapes and sizes, bringing into question the very definition of "normal. |
U.S. viewers (millions): million / Rating/Share: |
| 45 | | "" | Sara Charno | Mike Vejar | April 14, |
With Scully's help, Mulder investigates a strange death that he believes may be an example of poltergeist activity. |
U.S. viewers (millions): million / Rating/Share: |
| 46 | | "" | & | April 28, |
After several men in a prison die of a mysterious illness, Scully tries to discover the cause while Mulder attempts to find two escapees who could potentially spread the disease. |
U.S. viewers (millions): million / Rating/Share: |
| 47 | | "" | James A. Contner | May 5, |
Mulder and Scully encounter a man who is afraid of his own shadow. |
U.S. viewers (millions): million / Rating/Share: |
| 48 | | "" | May 12, |
Mulder and Scully investigate the disappearance of man in a town where the residents really are what they eat. |
U.S. viewers (millions): million / Rating/Share: |
| 49 | | ""‡ | Story by: & Teleplay by: | May 19, |
A computer hacker discovers evidence against the Syndicate that is so damning that its revelation to the public would be nothing short of catastrophic, leading Mulder into a race against sinister agents to learn the truth. (Part 1 of 3) |
U.S. viewers (millions): million / Rating/Share: |
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