The fifth season of X Files includes 20 episodes. 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) Redux
With everyone thingking Mulder has shot himself (you already know he didn’t since the show went on another 4 seasons so I’m not spoiling anything) he’s covertly hunting a cure for Scully’s cancer. He is now convinced that aliens are just a government cover and has lost all faith in the beliefs he once held so dear. Scully is put on the spot in an official investigation to reveal the identity of Mulder's informant.
-Title notes: “Redux” is Latin meaning “brought back.” In this case Mulder is brought back.
2) Redux 2
Scully has been rushed to the hospital, and Mulder reveals himself to check on her. He has come to suspect a villain in the FBI connected with Scully's plight. Scully believes it's Skinner that's dirty which is backed by others who want Mulder to put an end to the AD's career. Scully turns to prayer and faith for help.
-Title notes: This time it's Scully who is brought back.
3) Unusual Suspects
Flashback to when the Lone Gunmen first met and made friends with Mulder. A mysterious woman claims to be in trouble and seeks help from Byers who turns to Frohike and Langly as well. When Holly points to Mulder as being a pyscho the would-be heroes step in to stop him. Mulder is more or less a typical FBI agent and has no ties to anything odd just yet.
-This is a fun look back at Mulder's earlier days which we've heard referenced but not really seen. It's great to have a story focused on the Lone Gunmen. It won't be their last.
-Title notes: It's a reference to the phrase/movie title “The Usual Suspects” but referring to the Lone Gunmen who are being interrogated in this story.
4) Detour
Mulder & Scully investigate disappearances in the deep southern woods. As the members of their team disappear one by one the agents find themselves stranded in the wilderness with creatures who can remain virtually invisible as they take down their prey with frightening speed.
-Title notes: Mulder and Scully detour from where they are supposed to be going.
5) Post Modern Prometheus
This black and white Frankenstein type tale sets the agents about the business of investigating genetic tampering and misunderstood monsters.
-This has the feel of a fairy tale mixed with horror. It reminds me a little of Tim Burton.
-Title notes: This is an obvious reference to Mary Shelley's novel. Prometheus made men out of clay. The mad scientist in this story is making people in his own way.
6) Christmas Carol
Scully gets strange calls to help someone in trouble and stumbles across a suicide that she comes to believe is actually murder. With everyone from her own family to the victim's family to the cops questioning her motives she turns up evidence that can't be easily pushed aside. Did Scully's sister have a child that she hid from the family? Scully needs that answer, too.
-Title notes: The story happens at Christmas with voices from beyond. It's an obvious reference to the famous work by Dickens.
7) Emily
Scully discovers that a little girl involved with her previous investigation seems to be related to her. Emily is dying, and Mulder tries to find info on her condition while Scully struggles to keep her alive. There are inhuman things taking place here.
-Title notes: This is the name of the little girl.
8) Kitsunegari
Pusher returns. Is he taking revenge on those that incarcerated him or is something else going on? Mulder & Scully investigate the man that can control them with mere words.
-Title notes: This means "Fox hunt" and is left at crime scenes as a taunt for Mulder.
9) Schizogeny
People are being killed by nature. Are they abusive parents getting what they deserve? Maybe, but there’s something strange about the psychologist. The X agents investigate a troubled teen who seems to be the central focus, but the very trees seem to be against them.
-There are several different threads going on here: trees that bleed connected to something that happened years ago, a strange backstory for the villain who has mysterious powers which aren't explored outright very much, misdirection on the part of several characters, and the current plot which the agents are actively investigating. It's a lot to take in and might make more sense with a second viewing. Many consider it a terrible episode, some have even said it's the worst, but I rather like it and think it's miles ahead of such clunkers as “Space” or even “Aubrey.”
-Title notes: Many have assumed that this was supposed to be “schizogony” which has to do with asexual reproduction (which doesn't makes much sense in the context of this story). However, “schizogeny” is a word that has to do with plant cells separating to form cavities in which secretions gather (such as resin or oil). In this episode the trees secrete blood, and humans are trapped in earthen cavities created by the killer plantlife.
10) Chinga
Scully gets pulled into an investigation while on vacation. Violence seems to erupt in the wake of a young widow and her daughter. People believe she is some kind of witch, but there is something creepy about the kid and her dolly.
-I had looked forward to seeing this episode written by Stephen King, but while not bad it isn't as strong as I expected. Too much reliance on making the kid creepy (without really doing a good enough job) and overuse of the Hokey Pokey song weaken it. It does have some stunning special effects, though.
-Title notes: This is the name of the doll. It's also a Spanish profanity, which King says he didn't know at the time of the writing. Since it's also the name of a meteorite that fell in Siberia it's possible that King used that for inspiration instead of the Spanish word.
11) Kill Switch
Someone has created an extremely powerful artificial intelligence that will kill to survive. Now it’s trying to blow up Mulder & Scully who have the one thing that can kill it. With Mulder held captive and Scully chased by lasers from the sky survival doesn't look likely.
-Written by veteran novelist William Gibson this sci-fi thriller expertly packs a lot into its runtime. It feels like it should be longer than it is because it covers so much ground.
-Title notes: This is what Scully needs to kill the AI.
12) Bad Blood
Mulder drives a stake through a boy’s heart. Was he a vampire or did Mulder finally cross the line in his paranoia? Now the FBI is being sued. Mulder wants their stories straight so he and Scully take turns recounting the same events leading up to the disaster.
-I love a well done point-of-view story. We get a look into the perceptions of the different characters and how the same events can be seen completely differently - skewed by bias but not untrue. It's one of the funniest episodes of the entire series and a personal favorite of mine.
-Title notes: This is a reference to the feud between Ronnie and Mulder (or any number of other conflicts within the story) with a vampire nod.
13) Patient X
Cassandra Spender is the victim of multiple abductions. She turns to Mulder for help, but he’s still in doubt about such things. Her son Jeffrey, an FBI agent, wants Mulder to leave her alone and pushes the matter despite Mulder's desire to remain at arm's length anyway. Meanwhile former abductees are being summoned to particular gathering points where they are burned alive. Scully is among those being called.
-Title notes: A reference to an anonymous patient (spoken about in a lecture at the beginning of the episode) which turns out to be Cassandra.
14) The Red & The Black
The latest round of burn victims is being investigated, and this time there are survivors though they have no memory of what happened. Cassandra cannot be located amongst the living or the dead. Krycek faces off with the syndicate over a possible vaccine for the black oil.
-Title notes: This is a multi-reference title as these two colors are paired in numerous different works and games which can be connected directly or figuratively to this story. As such the meaning is probably intentionally subjective. Some obvious connections are a reference to the fire and oil which are icons of the opposing alien forces, or a game of strategy with one side represented by red and the other by black.
15) Travelers
Flashback: before Mulder got involved with the X Files he investigated a strange event that referenced his name. He seeks out Arthur Dales who tells the tale of an investigation into supposed Communists that turned into dealing with victims killed by having all their soft tissue dissolved from the inside. His superiors don't want the details known so the case is censored and buried under the filing of X.
-This is an outstanding episode in so many ways. I like the look into the history of the X Files, the change in pace and style without going the route of putting our starring actors into other roles, and the character of Dales.
-Title notes: There are a few applications of this one. “Fellow travelers” cooperate with an organization without having an actual membership in the group. In this general meaning the man Dales is hunting fits the description. The phrase is most closely associated with people who had commie sympathies during the McCarthy era which ties directly into this story. Also, the creatures that the killers carry can be considered travelers in the human bodies.
16) Mind’s Eye
A blind girl is accused of murder, but the facts just don’t add up. She has some kind of sight, it’s just not with her eyes. Mulder is the only one on her side, but she doesn't want any help from anyone.
-Title notes: The suspect sees through a sort of mental connection.
17) All Souls
Deformed girls, all sisters, are being killed as if struck down by God. Is it the strange priest or is he trying to protect the girls from the devil? Scully is pulled in and must deal with her emotions over the loss of Emily as she tries to save the remaining sister amongst stories of angels and demons.
-Title notes: Father Gregory mentions that good is losing the struggle for all souls (in the sense that Heaven and Hell are engaged in a battle that either could win). This is why he does what he does.
18) Pine Bluff Variant
Mulder gets involved with a terrorist organization. They are testing a biological agent that dissolves flesh. Scully wants to know if Mulder really has gone bad while the villains test Mulder's loyalty with potentially fatal consequences.
-There isn't much of a follow up to the plot. It's more of a suggestion than a real plot wrap up. It should have been revisited in later stories.
-Title notes: This is a reference to the location where the strain of bacteria was developed.
19) Folie A Deux
A man claims his boss is a monster, literally – a giant bug that turns humans into zombies that do his bidding. The problem is these monsters “hide in the light” so they can stand in front of most anyone and appear perfectly normal. Mulder must decide if the guy’s cheese slid off his cracker or if there’s some truth to it. When Mulder starts seeing strange things himself the only explanation is that he has bought into the insanity and must be confined.
-This is a great monster episode with creepy visuals.
-Title notes: "A madness shared by 2," this is the initial explanation of the events.
20) The End
Mulder and Scully stumble across Gibson Praise who can read minds as easily as other humans breathe. The syndicate wants the boy dead before he can expose their secrets; he could be the key to everything unexplained in the X Files. CSM will go to extreme lengths to stop Mulder this time.
-Title notes: This is the end of the X Files prior to the events of the movie. It marked the end of the filming in Vancouver, and by the end of the story Mulder's office is completely destroyed.