The first season of X Files includes 24 episodes counting the pilot. Production order doesn't always match airing order, but the TVD's follow the airing schedule which makes the most sense for story flow.
1) Pilot
When FBI agents Mulder and Scully are paired they immediately take on a case that will be typical of the type they will continue to investigate, but typical in their case is unfathomable in any other. Following leads on a mysterious death the agents exhume a buried corpse that turns out to be inhuman. Mulder suspects alien abduction with a government involvement. Finding evidence is hard enough, but now somebody out there is trying to actively prevent them from carrying out a successful investigation.
-Title notes: Pretty much all pilot episodes are called “Pilot.”
2) Deep Throat
When a test pilot develops a strange condition the military won’t comment on it even to his wife. When Mulder steps in to investigate a mysterious man approaches him to get him to drop it. But when does Mulder ever listen to admonition? Suspecting the involvement of alien technology, Mulder will get answers even if it means sneaking onto a top-secret Air Force base. There he’ll get a glimpse of what the military is hiding and just how far they’ll go to keep it a secret.
-Seth Green plays a small part. It’s amusing though definitely not his best work.
-Title notes: This is the code name for Mulder’s informant – a reference to a real life informant.
3) Squeeze
A business man is murdered in his office. That much is unquestionable; the rest is unexplainable. How did the killer get in? Why take the victim’s liver? When the investigative team hits a brick wall the lead investigator approaches Scully for help. He’s adamant about keeping Mulder out of it, but Mulder is the only one able to turn up any evidence, impossible evidence though it may be, which he then connects to old cases buried in the X Files. Just try keeping him away now.
-Doug Hutchison makes his first appearance as Tooms and Donal Logue guest stars.
-Title notes: This is a reference to the villain’s special ability.
4) Conduit
A teen girl vanishes from a camp site. She’s a wild child so chances are she ran off with some guy, but her mother thinks she was abducted. Mulder, feeling a special connection to the abduction of his sister, is the only person who is even willing to consider the possibility of inhuman kidnappers. The only witness, though, is a little boy who begins acting strangely mainly by writing in binary which turns out to be anything but random. That does get a few people’s attention much to Mulder’s dismay.
-Title notes: Mulder considers the boy to be a conduit for extraterrestrial info.
5) The Jersey Devil
A man is attacked and mutilated with teeth marks that appear to be human. The locals don’t want help with the case, but Mulder is too invested to back off. He sends Scully off while he plays homeless to find a monster – possibly the legendary Jersey Devil.
-This is one of the weakest episodes. For one thing more connection to the real Jersey Devil legend would have been an improvement. Besides not liking where the story goes with its explanation there just isn’t enough in the way of suspenseful elements. The emotional reveal of Mulder’s personality is good, though.
-Title notes: It's a real-life monster myth which locals attribute to the strange happenings.
6) Shadows
Mulder and Scully are called in to advise on the mysterious deaths of two criminals. Finding evidence of things the other investigators wouldn’t believe Mulder takes Scully on a fact-finding mission. They find an emotionally distraught woman surrounded by strange occurrences. An uncontrollable psychokinetic power? A sinister plot involving a faked death? Mulder is the only one with a chance to uncover the truth, but he may be prevented from doing so.
-Title notes: It's a reference to the intangible cause of the strange events compared to the tangible case of illegal dealings with terrorists.
7) Ghost in the Machine
A corporate exec. threatens to shut down a technology research project and is then mysteriously killed. A brilliantly masterminded plot or something less easily explainable? Mulder’s former partner calls on him for help and quickly displays the reason he doesn’t share Mulder’s respect like Scully does. The agents must find a way into a highly secured building guarded by a sophisticated and lethal computerized defense system before more die.
-Title notes: It's a parallel between human beings (this was Descartes' description of consciousness) and the sophistication of the computer’s intelligence.
8) Ice
A group of researchers dies mysteriously in an isolated facility. A nonsensical transmission is the only clue. Mulder and Scully along with a team of scientists are sent to investigate. They discover something so dangerous that they do not risk accidentally transporting it back to civilization. When people start dying the team quickly discovers that they can’t trust each other, but with the deadly blizzard raging outside they have nowhere to run.
-Xander Berkley guest stars.
-Title notes: The story revolves around ice.
9) Space
Someone or something is apparently sabotaging the space program shortly after some scientists begin seriously suspecting life on Mars. When a shuttle is launched on a mission a frightening vision causes an accident. If Mulder and Scully can’t figure out what’s going on in time to allow for repair of the shuttle the astronauts will die. Are Martians trying to hide their existence?
-The quality of this one lacks. It looks like an early 80’s or even 70’s TV show at first. There is none of the suspenseful atmosphere that has made so many other episodes great. This one might be the worst episode ever made.
-Tom McBeath (well known to Stargate SG1 fans) plays his first role. He’ll return a few more times though not as the same character. I guess they didn’t expect him to turn out to be such a recognizable face (as many of you read this and say, “Who??”)
-Title notes: The episode revolves around the space program.
10) Fallen Angel
A ship has crash landed and a secret government containment team dispatched. Deep Throat puts Mulder on the scent. When the agent is captured he meets another would-be investigator, Max. As Mulder tries to figure out the mystery of the ship and how Max fits in, a dangerous alien wreaks havoc on those that would try to capture it.
-Title notes: This is the government’s code name for the situation – a downed UFO.
11) Eve
A man is found dead, drained of blood. The work of aliens? Mulder thinks so and is hot on the trail. When a similar murder happens elsewhere the agents find that the man’s daughter looks identical to the first man’s yet there seems to be no relation between the two. They uncover a plot of genetic tampering (a precursor to the experiments revealed in later seasons) that some will kill to protect.
-This isn’t directly tied into the larger story that is to come but does seem to relate. Surprisingly none of the villains ever return to the series which is really too bad because the little girls are very creepy and do a terrific job with their roles.
-Title notes: This is the name of the villain.
12) Fire
A killer is targeting a prominent family, but how is he able to make things burst into flame with no discernible cause? An old flame of Mulder’s, Phoebe, comes to him for help, but the passions she stirs in him have a history of getting him burned. Mulder must face his fear of fire and a woman that likes to play games with his emotions.
-I’m very surprised there has never been another mention of Phoebe in the series. It actually weakens the impact of the story when you step back and look at the whole thing particularly in light of Mulder’s history with Diana. It makes Phoebe seem less important to him than this episode makes her out to be.
-Amanda Pays guest stars.
-Title notes: The episode revolves around fire.
13) Beyond the Sea
Scully sees her dad moments before she gets a call letting her know that he has died. Meanwhile Mulder is looking into a kidnapping that follows the MO of another case that ended in murder. A man on death row claims to have clairvoyant knowledge which he offers in exchange for a lighter sentence. The agents’ roles are reversed. Mulder is skeptical while Scully is not so immediately dismissive, but the grief over her loss may be clouding her judgment. Either way it’s a race to save the victims while Scully struggles with her loss.
-Brad Dourif guest stars as the inmate. Don S. Davis (General Hammond!!) plays Scully's dad.
-Title notes: It’s the name of the song played at Scully’s dad’s funeral and highlights his connection to the sea as well as his passing in life.
14) Gender Bender
A killer or group of them using sex as a weapon? The facts of the case are hard to reconcile, but that is Mulder’s specialty. The leads point to a secluded religious community whose strange ways and private nature hide dark secrets. A late night infiltration puts Scully in the hands of one of the cult members and Mulder in a hellish cave.
-The swap from horror to sci-fi towards the end doesn’t work very well.
-Nick Lea makes his first appearance, but it isn’t as Krycek.
-Title notes: This is a reference to the cross-gender nature of the villain.
15) Lazarus
Scully is involved with the stopping of a bank heist and loses a fellow agent, one with some personal ties to her. Attempts to revive the agent are successful, but he doesn’t seem to be himself. In fact, he’s acting like a criminal. Scully is quick to discount any strange events, but Mulder is too intrigued. And it’s a good thing because Scully is about to get herself in a world of trouble.
-Title notes: The character comes back from the dead so the title references the man raised from the dead by Christ.
16) Young at Heart
A criminal Mulder incarcerated is seemingly back from the dead with a vendetta against his captor. Memories of a difficult past weight heavily on the agent, but he can’t let up because the villain’s next target is Scully. What strange youth experiments were done on this man?
-Title notes: It's a reference to the youth experiments conducted.
17) EBE
A UFO is shot down by a fighter jet and a trucker may have answers, but when Mulder and Scully investigate the locals get uncooperative quickly. Mulder turns to the Lone Gunmen for help in tracking the potential path of the UFO while Scully investigates electronics she finds hidden in her pen. Mulder catches Deep Throat in a lie putting a kink in their relationship. How can Mulder trust him now? But nothing will prevent Mulder from finding his alien.
-Title notes: This stands for “extraterrestrial biological entity” which is what Mulder and Scully are chasing.
18) Miracle Man
A young man displays an aptitude for faith healing even to the point of bringing a burn victim back from the dead. Lately though, people he tries to help are dropping dead. Some think he’s at best a fraud, but others wonder what sinister motives his benevolence may hide.
-Title notes: This is a popular descriptor of someone who can perform miracles used here in reference to the boy's ability to heal.
19) Shapes
A werewolf story, X Files style. Something has been attacking animals, but when the monster is shot it turns out to be nothing more than a human. Was this an excuse to commit murder or is something more mysterious going on?
-Title notes: This is a reference to the shape-shifting ability – from man to wolf.
20) Darkness Falls
Mulder and Scully have a penchant for getting themselves into isolated areas in deadly situations. This time they are deep in the woods investigating the disappearance of an entire logging camp. Prime suspect: ecoterrorists. If only it were that easy to explain. An unknown bug has everyone living in fear, and though they’re not to blame for any deaths, the ecoterrorists have made escape impossible and survival unlikely.
-Title notes: This is reference to the onset of danger.
21) Tooms
Our first sequel, and they couldn’t have chosen a better villain to revisit. Resulting from evidence too crazy to believe, Tooms is released. FBI Assistant Director Skinner cracks down on the X agents essentially tying their hands in the matter under the watchful eye of CSM who appears to have it in for the X Files department. Mulder defies them in order to keep Tooms from killing again while Scully looks for easier to swallow evidence from previous murders to put him away. Tooms is fighting back though, framing Mulder for assault.
-Title notes: It's the name of the villain.
22) Born Again
A lost and withdrawn little kid shows up outside a police station. Moments later an officer dies a strange death involving a high window. As Mulder and Scully investigate they find that this troubled girl is the center of many strange events. When they find a link to a murdered cop some years before the mystery gets increasingly sinister.
-Maggie Wheeler guest stars.
-Title notes: A deceased person is essentially born into a new body. There doesn’t seem to be any connections to the Christian use of the phrase.
23) Roland
A seemingly mild-mannered and simple-minded janitor murders a scientist and solves complex equations. It’s up to the FBI to figure out what’s really going on.
-Title notes: It's the name of the janitor.
24) The Erlenmeyer Flask
A man with superhuman powers evades cops then vanishes. Deep Throat gets Mulder involved who finds his way to a genetic scientist – a suspiciously dead one. Mulder uncovers a cloning operation while Scully finds a strange virus with unearthly genetic structure. The perpetrators are deadly serious about hiding their agenda, and they raise the stakes with Mulder’s life.
-Title notes: This is the type of container that holds what Scully is afraid will turn out to be monkey pee.