3.1 "The Blessing Way"
The Smoking Man works quickly to recover the stolen computer files, but finds himself thwarted by a man whom he hope is dead. Meanwhile, Scully finds herself at a loss for her next step and turns to her family for support, since Mulder is otherwise engaged fighting for survival. Part two of three.
3.2 "Paper Clip"
Reunited, Mulder and Scully locate an old scientist from Nazi Germany, pardoned through Operation Paper Clip. The information he gives them leads to their discovery of something which could mean their deaths. Part three of three.
Mulder is skeptical over a coroner's report regarding the fifth person to be struck by lightning in a small Oklahoma town. Their investigation into the latest death seems to point to the only person to have survived a lightning strike, an emotionally-charged youth.
3.4 "Clyde Bruckman's Final Repose"
Skeptical of a famous psychic's predictions regarding the murder of several prognosticators, Mulder instead finds someone who he believes truly can predict the future. Though catching the killer could prove difficult, particularly if the murderer can also see into his future.
3.5 "The List"
A death row inmate's promise of reincarnation for the purpose of avenging the injustice of his execution begins to be fulfilled with the death of one of the Florida prison's guards. The fear of his retribution has everyone scrambling to determine if they are on the list of his five victims, including Mulder and Scully who are trying to determine how he has returned to execute his tormentors.
Meeting insecure women through an on-line service, a serial killer seduces his prey with the right words. However, Mulder and Scully determine these killings are far from ordinary by the presence of a strange substance coating the victims, a substance which seems to digest the fatty acids in flesh.
3.7 "The Walk"
Another failed suicide attempt by a patient in a military hospital interests Mulder with the talk of a "phantom soldier" which has prevented the man's death. The general in charge is at first opposed to the FBI's involvement until the invisible killer begins stalking him. But none believe when the primary suspect is a quadraplegic.
When a young girl is kidnapped from her home, a fast food worker miles away collapse on the job, apparently experiencing exactly what the child is feeling. When Mulder learns that the woman was kidnapped and held hostage for years as a child, he begins to believe that she may be the key to help find the missing girl.
A mail order videotape of an alien autopsy blossoms into a much more complicated investigation when Mulder and Scully find the distributor of the tape murdered in his own home apparently by a high-ranking Japanese diplomat. Following up individual leads, Scully finds herself recognized by complete strangers while Mulder tries to find out more about the origin of the video. Part one of two.
Scully takes X's advice to heart and investigates more into the implant she removed from her neck. Mulder, having ignored the advice given him, finds himself trapped on the train with a Japanese scientist and the man sent to kill him. Part two of two.
A search for stigmatics turns up a young boy in Ohio whom Mulder and Scully immediate travel to protect. They feel that he may be the next choice of a fanatic who has murdered eleven people claiming to be stigmatics. But when it appears that this boy may be legitimate, Scully starts believing she was the one who was chosen.
3.12 "War of the Coprophages"
While waiting out the fumigation of his apartment, Mulder stumbles into a Massachusetts town where it appears that cockroaches have been attacking and killing several residents. Upon consulting Scully, he is told that it's probably just a load of crap.
The murder of several high school students in the small town are believed to be the work of a Satanic cult through the machinations of the two girls truly at fault. The tension between Mulder and Scully and that of the townsfolk rises because of the fear and anger, though an astrologer insists it's because it is written in the stars.
A three year murder investigation by one of the FBI's finest behavioral scientists comes to a close with the arrest of an artist who claims to have been possessed by an evil force. But when the deaths continue, it is up to Mulder to get inside the killer's head to find this gargoyle.
3.15 "Piper Maru"
The crew of the salvage ship Piper Maru return with severe radiation burns after a visit to the same location as a previous vessel, the Talypus; a ship in which Mulder is very interested. Scully's thoughts return to her murdered sister as she goes to the naval base where she grew up to question an old neighbor if he knows anything about the undersea location. Part one of two.
Mulder returns from Hong Kong with the hopes of retrieving the lost digital tape, only to have Krycek slip from his grasp. Meanwhile Scully spearheads the investigation of Skinner's attacker in the hopes that it will resolve the case of her sister's murder. Part two of two.
A man is apprehended yet escapes after he claims to be the hired killer of 14 people whose deaths had previously been ruled as suicides. The man, who seems to have the ability to control others, desires a challenge, leaving clues for Mulder and Scully to follow as he sets up his contest of wills.
3.18 "Teso Dos Bichos"
After two people associated with a sacred artifact disappear, Mulder and Scully investigate the apparent curse caused by the unearthing and relocation of the remains of an amaru, a female shaman. Their lead suspect is a member of the dig which brought the amaru to the US, though he is more preoccupied with using a native hallucinogen to pray to the spirit.
3.19 "Hell Money"
When the night watchmen discovers a man being burned alive in a funeral home, it brings Mulder and Scully to investigate the deaths of many Chinese immigrants in the San Francisco bay area. With the aid of a Cantonese speaking detective, they chance upon the clues which lead them to a game where you truly bet your life.
3.20 "Jose Chung's 'From Outer Space'"
Scully takes advantage of an opportunity to meet the famous writer, Jose Chung, who wishes to interview her and Mulder for his latest book on alien abduction. He has come to obtain her take on the apparent abduction of two teenagers and two grey aliens by the Lord Kinbote.
Dealing with having to sign the divorce papers from his wife, Assistant Director Skinner inadvertantly spends the night with a prostitute and wakes the next morning to find her dead by his side. Unable to explain the events, he half-believes he may have killed the woman, but Mulder and Scully refuse to accept that as truth.
The disappearance of a federal wildlife official gives Mulder the excuse he needs in order to drag Scully down to Georgia with him. They come in search of the local legend "Big Blue," an aquatic dinosaur reputed to inhabit the local lake.
3.A "More Secrets of the X-Files"
A second retrospective recapping the highlights of the first three seasons, focusing on the ongoing government conspiracy plotlines.
Mulder and Scully investigate a series of murders in a Maryland town where it isn't caused by too much violence on television--it's simply caused by television. While Scully finds herself mesmerized by the recordings the murderers kept, Mulder sets out to prove it isn't what you see on TV, but what you don't.
3.24 "Talitha Cumi"
A disgruntled worker starts an incident where four people are shot, but a mysterious man miraculously heals them all before vanishing. Mulder and Scully begin work on the case when Mulder receives word that his mother was admitted to the hospital. Discovering she recently met with the Smoking Man, he feels certain the two events are related. So, he begins his search for the healer, but he is not the only hunter. Part one of two.