The third season of X Files includes 24 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) The Blessing Way
Mulder is missing. CSM is willing to rough people up in an effort to find him and even resorts to taking Scully’s files at gunpoint. Mulder is found by the local Navajo, but his life hangs by a thread. As they try to help him recover Scully finds a microchip implanted in her neck. Well Manicured Man warns Scully of the extreme danger she’s in, and she suspects Skinner of being sent to assassinate her.
-Title notes: This is the ritual used to help Mulder.
2) Paper Clip
When Skinner proves his loyalties Mulder and Scully set out to nail the conspirators. They find a scientist who performed experiments under the guide of the State Dept. This may be the hybrid creation project that resulted in the mass of alien corpses in the train car. This leads the X agents to a repository of information that is almost beyond imagination. Meanwhile CSM finds himself under heavy scrutiny from the Syndicate. He is ready to take drastic measures to save face, and this puts the agents in his crosshairs.
-Title notes: This is the code name of the operation Mulder and Scully uncover.
3) DPO
Darin is troubled kid can control lightning, and he aims to use it to get whatever he wants namely his very hot but very happily married teacher. Mulder and Scully are investigating the strange deaths around town, but as they close in on the killer they have to wonder how you stop a killer that can fry you just by thinking about it.
-Giovanni Ribisi and Jack Black guest star.
-Title notes: These are the initials of the killer which is the vital clue in finding him.
4) Clyde Bruckman’s Final Repose
A psychotic psychic is killing other psychics in gruesome ways. After Mulder and Sully clash with a phony TV psychic they stumble across a real one, Clyde, who, reluctant as he is, may be their only hope in catching the killer.
-Peter Boyle has a sizable role.
-Title notes: This is a reference to Clyde’s death.
5) The List
A man on death row threatens to come back from beyond the grave to take revenge on those that mistreated him in life. Baloney right? Maybe not because people start dropping dead mysteriously. But is it a ghost or just a clever plan with a little help from the living? Mulder and Scully are at odds over the explanation as usual, and it doesn’t help that the prison warden and guards have secrets to hide.
-Title notes: The episode centers on the list of people that are slated for death.
6) 2shy
A man is meeting women on the internet and killing them in inhuman ways. They are essentially dissolved and their fatty tissue consumed. Mulder and Scully set after him but underestimate his resourcefulness.
-Title notes: It's the username of the monster.
7) The Walk
A man is trying to kill himself but claims someone won’t let him die. Even boiling himself doesn’t work. Mulder and Scully bump heads with military security in their investigation, but Mulder may just be the General’s best chance at stopping this madness. But could the quadruple amputee Mulder suspects really have anything to do with what’s going on? I mean the guy has no arms and no legs!
-When Mulder and Scully get pushed around by the military it’s nice to see them finally get the chance to push back and win a round. There is some particularly good acting in this one.
-Title notes: This is a double-meaning. “Taking the walk” is sometimes used in reference to death such as going to one's execution or committing suicide which is what some of the characters here are trying to do. Meanwhile, the man Mulder suspects has no legs and can't walk.
8) Oubliette
A man working with a photographer has an obsession with a pretty young girl, enough to go so far as to kidnap her. At the same time a woman across town collapses while reciting the lines of the kidnapper. Mulder is interested for obvious reasons, but everybody else suspects complicity. If he lets them take her into custody he loses his only connection to the missing girl. But is he just getting caught up emotionally because of the young sister he lost himself?
-A nice bit of irony shows up when the mother of the missing girl assumes Mulder can’t possibly know what it’s like to lose someone like that. Little does she know. Of course, it’s just an emotional response, but it is a good reminder that you never know what someone may have been through.
-Jewel Staite guest stars.
-Title notes: The kidnapped girl is held captive in an oubliette-type room.
9) Nisei
Doctors working on an alien in a secret lab are gunned down, but a video leaks out and Mulder manages to get a copy. While he investigates Scully runs across a group of women that share her abduction experience – all with implants. They tell her she will develop cancer as a result of what was done. Mulder’s trail leads him to chasing train cars full of doctors. Are these guys responsible for what happened to Scully? But that would mean it wasn’t aliens that abducted her. Against X’s admonition Mulder boards a train to find the answers…… to be continued…….
-Title notes: This is the label given to the offspring of a Japanese couple when born outside of Japan. The literal translation is “second generation” which can be used to describe the hybrid creations.
10) 731
We’re not picking up where we left off last time, but we’ll get there. First we need to visit a group of strange looking people who are taken from a secluded disease facility and executed. X approaches Scully encouraging her to look deeper into her implant. It’s a chip for reading and implanting brain waves (Scully has no imagination for this sort of thing; that would have been my first and immediate guess). Meanwhile Mulder hunts for scientists on the train he boarded, but an assassin is on the hunt as well. When Mulder confronts him he claims there’s a bomb on the train. Scully finds more terrestrial answers to her experiences while Mulder tries to figure out what is on the train with him before it blows up.
-Title notes: This refers to the unit of scientists experimenting on people. There’s a historical reference to WWII scientists experimenting on POW's
.11) Revelations
A preacher talking about miracles displays divine stigmata shortly before he is killed by someone with superhuman abilities. He’s posthumously proven to be a fake. If the killer finds a real stigmatic can he bring about the end of the world? When a boy displaying stigmata seems to be the real thing, he is kidnapped. Mulder and Scully play opposite roles this time; she believes while he doesn’t.
-I like the role reversal of Mulder and Scully on occasion, but why does Mulder always have to disbelieve when Scully believes and vice-versa? I think it would be nice to have them on the same side from time to time or maybe Scully believing God while Mulder believes aliens. Besides that we got through with an episode not too long ago where Scully had a hard time believing in the supernatural even where God was concerned. This inconsistency is one of my biggest gripes about the show. I do like the spiritual wrap –up in this episode. “I’m afraid God is speaking, but no one’s listening.” I feel like that a lot.
-Title notes: This is taken from one of Mulder’s lines. It’s a reference to the Biblical book and seems to refer to the threat of the end times though it involves nothing like the prophecies from the book.
12) War Of The Coprophages
Are cockroaches fatally attacking people? Mulder turns up some strange evidence that leads him to a scientist who believes that alien explorers would come in insectile form. Is this what Mulder has uncovered? Hopefully the drop-dead gorgeous entomologist, Bambi, can help him figure it out.
-Here’s a good example of what I was talking about earlier. Right after Scully’s expressed religious views comes some views on the origins of life that have no hint of any involvement by God and do not line up with the Bible. This isn’t a religious show so I don’t expect a Creationist’s view of the universe, although as many times as God and the Devil show up in the series I’m surprised there isn’t at least some debate on the matter. We’ll be visiting this subject again in later seasons. However, for the sake of Scully’s established religious beliefs there should be at bare minimum questions about how God fits into the emergence of life or the expression of such a Godless process of evolution from a viewpoint other than hers.
-Title notes: This is a roach reference and their apparent desire to kill humans.
13) Syzygy
Some kids think a cult is out to get them. When a boy is found dead while two girls laugh and joke about it some call satanic ritual while others say bull. As they investigate Scully becomes extremely testy while Mulder is distant and uncaring. She takes up smoking while he starts drinking all the while fighting like a dysfunctional married couple. What can be powerful enough to affect he very personalities of the agents, and not only them but an entire town? Could it be written in the stars?
-This is one of my least favorite episodes this season. I just didn’t find it particularly gripping. For one thing the teen girls are very stereotypical in the extreme and unbelievable. I’m sure this is supposed to be tongue-in-cheek humor, but I’ve never cared for that much.
-Ryan Reynolds has a small role.
-Title notes: This term deals with alignment of celestial bodies which is at the core of the story.
14) Grotesque
When a model is attacked after a strange session with a painter, the artist is arrested. He claims it was a demon. When the killings continue he claims that the demon is using someone else. Mulder clashes with the lead investigator, but it’s possible the guy requested Mulder’s involvement out of a secret respect. As Mulder becomes withdrawn during the investigation Scully begins to worry about him. Evidence begins to point to him being under the control of if not the demon then the hysteria created by the killer’s insanity. Maybe Mulder has gone too far into his mind.
-This is one of the stranger episodes of the series. It’s hard to follow, and took me a couple of viewings to really get it. It’s pretty spooky, though, with one of the darkest atmospheres of any episode this season.
-Kurtwood Smith guest stars.
-Title notes: There are a few objective and subjective applications of this word. The molds we see fit the description of a “grotesque” (noun, not adjective) more than a “gargoyle” even though we have come to think of grotesques as gargoyles. It can also be applied as an adjective to describe the artwork and the darkness invading the hearts of the characters.
15) Piper Maru
Divers find a sunken plane whose pilot is impossibly alive. What they can’t know is that the poor fool is infected by the black oil – a sentient (or at least semi-so, I’m not sure that is ever specifically stated) alien organism that can enter and control a human host. Meanwhile the hunt for Melissa’s killer is called off, and Scully takes it hard. There’s no rest, though. She has to get to work when the sailors from earlier turn up with severe radiation burns. She uncovers an old story with striking similarities to the one unfolding and sets out to find more. Mulder is also investigating and turns up a murderous plot tied to the selling of secrets by Krycek. They’ll have their own dealings with the black oil soon. Back in the U.S.A. Skinner is shot when he continues looking into Melissa’s death for Scully.
-This is, as you may have already guessed, the introduction to the black oil which will play such a vital role in the mythology.
-Title notes: This is the name of the ship in the episode (named after Gillian Anderson's daughter).
16) Apocrypha
A bed-ridden sailor tells the end of the story Scully turned up earlier, but it’s not Scully he’s telling it to, it’s someone whose motives are less clear. Scene shift: Scully watches over the injured Skinner while Mulder takes Krycek off to retrieve the digital tape the villain took off Skinner back several episodes ago. Everybody starts figuring out what’s going on. The Syndicate realizes someone is selling their secrets and that events are tied to the old tale of the oil. The Syndicate is none to happy with Cigarette Smoking Man and his handling of the situations. Scully starts making ties between Skinner, her sister, and the forces that stopped her murder investigation.
-This is a welcome follow-up to Scully’s loss.
-Title notes: “Apocrypha” means “hidden things” which applies to the secret story of the sailors and the secrets on the digital tape. The Apocrypha as a book contains writings that some consider to be questionable at best while others think it sheds new light on biblical history which would apply to the information revealed in the episode.
17) Pusher
Modell is a killer whose M.O. is talking a person into doing themselves in. How can Mulder and Scully catch someone who can manipulate law enforcement and the entire judicial system with a word? Modell just plays games with the FBI and the X agents are in his crosshairs.
-There’s a nice reference to Flukeman in here.
-Title notes: It's what the villain calls himself – he pushes his will on others.
18) Teso Dos Bichos
An excavation team disturbs the corpse of an ancient female shaman. Soon thereafter people in contact with the body start dying mysteriously, or disappearing leaving only blood behind would be more accurate. Is a feline spirit controlled by the dead shaman devouring people or is it the work of a deranged scientist high on some kind of native mixture?
-Frank Welker, one of my favorite voice actors, provides the cat noises.
-Title notes: The translation is “burial mound of small animals” and is a reference to the dig site.
19) Hell Money
Somebody is cremating people alive in Chinatown. Some suspect a gang, others believe in ghosts. Enlisting the help of a local Chinese detective the X agents uncover a dangerous underground game in which people gamble for money with body parts.
-Lucy Liu and BD Wong guest star.
-Title notes: This is a Chinese offering to evil ghosts.
20) Jose Chung’s From Outer Space
Jose Chung is researching an alleged abduction for a new book he’s writing. What he comes up with are conflicting reports, some pointing to true abduction, others suggesting an attempt to cover up a rape, and plenty claiming pure delusion. Scully recounts her experiences and the evidence.
-This is a wild and confusing episode though very humorous. It’s anyone’s guess what really happened as there seems to be elements of truth in the various stories, but separating truth from lie (or just misconception) isn’t always easy. One of the funniest moments in X Files history is when Mulder screams at the sight of a corpse.
-Charles Nelson Reilly plays Jose. Alex Trebek and Jesse Ventura play J and K, ok not really but they do play men in black.
-Title notes: It's the name of the writer and the title of his book.
21) Avatar
Skinner is struggling with ending his marriage. As he's sorting things out he meets a woman in a bar then wakes up next to her dead, naked body. The X agents jump in to figure out what’s happening. Skinner can’t be a killer can he? It’s not looking good for Skinner especially when someone, supposedly him, runs his wife off the road landing her in the hospital, yet he doesn’t want any help. What’s up with him anyway?
-While a good episode except for a few nitpicks, I don’t recall any hint whatsoever of Skinner having a wife past or present throughout the rest of the series. Coming back to this episode knowing that weakens its impact. Some sort of followup would have made a big difference.
-Amanda Tapping, Samantha Carter to those of you not fortunate enough to be inducted into the Stargate SG1 family, puts in an appearance. It’s hard to buy her as a prostitute, though.
-Title notes: This is a reference to the spiritual help Skinner is given by a spirit or avatar.
22) Quagmire
It’s Mulder and Scully vs. Nessie – the Loch Ness Monster. OK, not quite, but Mulder believes a similar creature is killing people. Scully is trying to figure out what is “really” going on. When their boat is sunk by something big they are left stranded in the water with a hungry monster nearby. The ending provides some good material for debate.
-See this is what I don’t understand. We can get references throughout the series to Scully’s dog whom she loses in this episode but no mention whatsoever of Skinner’s wife or Phoebe from "Fire?"
-Title notes: The term refers to soggy ground which is where the bulk of the episode takes place.
23) Wetwired
An insane man is killing people he thinks are the same sadistic murderer who keeps coming back. Mulder reluctantly takes on the case simply for the hope of saving lives. Could people be getting brainwashed by their TV’s? Mulder begins acting strangely, cavorting with CSM and such, leading Scully to take “trust no one” to new extremes.
-Title notes: This is a reference to the “wiring” in a person’s head in connection to the technology used to alter it.
24) Talitha Cumi
When a gunman shoots several people a man steps out of the crowd to miraculously heal the wounded. The X agents investigate, but the miracle worker has disappeared without a trace. Mulder’s mom ends up in the hospital. As Mulder tries to decipher the cryptic clue she tries to give him he must also unravel the mystery of why she would be meeting with CSM. What is his role in her crisis of health? The agents have once again come across the cloning/colonization plot and the bounty hunter is on another killing spree.
-Title notes: A phrase that mean “arise maiden” or “wake up, little girl” depending on who's translating (an Aramaic command used by Jesus in Mark 5:41) - this is a reference to Jeremiah Smith’s miraculous ability.