Season 3 introduced the Syndicate, a powerful covert organization covering up the existence of extraterrestrial life. The Syndicate would remain the primary antagonists up until season six. The abduction theme of the mythology arc concludes at the beginning of the season, with focus shifting to the black oil.
Episodes marked with a double dagger (‡) are episodes in the series' Alien Mythology arc.
|No.||Episode Name / Summary|
|3x01||"The Blessing Way"‡
As Navajo Indians try to save Mulder from death, Scully comes to terms with her assumption that he has already died and is warned that her own life is in danger. (Part 2 of 3)
After Mulder and Scully are reunited, they investigate a photograph that seems to connect Mulder's father to experiments that were conducted after World War II but used scientific knowledge from Nazi Germany. (Part 3 of 3)
Mulder and Scully investigate the deaths of several people who were struck by lightning.
|3x04||"Clyde Bruckman's Final Repose"
Mulder and Scully receive help in a murder case from a reluctant psychic.
A man about to be executed by electric chair vows to return to kill five men who wronged him in prison.
Several women disappear after meeting someone in Internet chat rooms.
The astral projection of a soldier begins killing several people in and around a military hospital, apparently in search of revenge.
A young girl is kidnapped and appears to have a psychic connection to a woman who was kidnapped many years before that manifests in mirrored actions miles away.
Investigating a video of an alien autopsy, Mulder and Scully find evidence that Japanese scientists brought to America after the Second World War may have been involved in Scully's abduction. (Part 1 of 2)
Mulder is trapped on a train carriage with a ticking bomb and a killer who claims to be an NSA agent. (Part 2 of 2)
Mulder and Scully investigate a series of murders that may be related to stigmata and Scully questions her faith.
|3x12||"War of the Coprophages"
Mulder gets caught up investigating what could be super-human cockroaches with metal bodies.
Mulder and Scully investigate strange murders in New Hampshire that may be due to a rare planetary alignment.
Scully becomes very concerned as Mulder gets more and more involved with a case that may involve demonic possession.
When a diver from a French salvage ship called the Piper Maru discovers a World War II fighter plane and is the only member of his crew not exposed to harmfully extreme levels of radiation, Mulder and Scully investigate. (Part 1 of 2)
The assassin who killed Scully's sister is finally captured after shooting Skinner while Mulder and Scully search for Alex Krycek, who has been infested with a strange alien parasite. (Part 2 of 2)
Mulder and Scully struggle to capture a dying man who can apparently bend others to his will and convince his victims to place themselves in extreme danger.
|3x18||"Teso Dos Bichos"
When a Sokona Indian burial urn is removed from the Ecuadorian highlands, a series of unexplained deaths follows three weeks later. Mulder investigates the case with Scully and soon comes to the conclusion that the deaths were caused by a curse of the jaguar spirit.
In Chinatown, Mulder and Scully discover an illegal lottery in which the "losers" are forced to donate their internal organs.
|3x20||"José Chung's From Outer Space"
An alien abduction of two teenagers with different versions of the same facts prompts a science-fiction novelist to write a book about the incident. However, no one involved with the investigation can tell him the full story with any accuracy.
During a one-night stand in the midst of his divorce, AD Skinner becomes a murder suspect. Mulder and Scully return the many favours that he has done for them by trying to determine what actually happened, all the while discovering more about Skinner's personal affairs.
In a small town, Mulder and Scully investigate rumors of a prehistoric lake monster called Big Blue.
As the agents investigate a series of murders committed by ordinary citizens angered after seeing illusory images, Scully's trust in Mulder is put to the ultimate test.
While Scully researches a man with extraordinary healing abilities named Jeremiah Smith, Mulder finds evidence of a deadly alien bounty hunter. (Part 1 of 2)
- David Duchovny as Special Agent Fox Mulder (24/24 episodes)
- Gillian Anderson as Special Agent Dana Scully (24/24 episodes)
- Mitch Pileggi as Assistant Director Walter Skinner (10/24 episodes)
- William B. Davis as Cigarette Smoking Man (7/24 episodes)
- Tom Braidwood as Melvin Frohike (5/24 episodes)
- Bruce Harwood as John Byers (4/24 episodes)
- Dean Haglund as Richard Langly (4/24 episodes)
- Nicholas Lea as Alex Krycek (4/24 episodes)
- Brendan Beiser as Pendrell (4/24 episodes)
- Lenno Britos as Luis Cardinal (4/24 episodes)
- Don S. Williams as First Elder (4/24 episodes)
- Steven Williams as X (4/24 episodes)
- Sheila Larken as Margaret Scully (3/24 episodes)
- John Neville as Well-Manicured Man (3/24 episodes)
- Rebecca Toolan as Teena Mulder (3/24 episodes)
- Peter Donat as William Mulder (2/24 episodes)
- Jerry Hardin as Deep Throat (2/24 episodes)
- Melinda McGraw as Melissa Scully (2/24 episodes)
- Stephen McHattie as Red-Haired Man (2/24 episodes)
- Morris Panych as Grey-Haired Man (2/24 episodes)
- Floyd "Red Crow" Westerman as Albert Hosteen (2/24 episodes)
- Michael David Simms as Senior FBI Agent (2/24 episodes)
- Robert Ito as Dr. Takeo Ishimaru/Shiro Zama (2/24 episodes)