| Season | Series | Image | Title | Writer | Director | Original Airdate | 
|---|
|  | 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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