The sixth season of X Files includes 22 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 Beginning
Tying in to the movie, Mulder is hunting down an alien created by the black oil even though he’s been pulled from the X Files. Is Fowley helping him or playing him? Gibson is used by the syndicate to track the same creature while Scully investigates the boy’s DNA.
-Title notes: This is essentially a new beginning for both the series and the characters.
2) Drive
A man must move West at high speeds or his head will explode. Everyone thinks he's a criminal rather than a victim so in order to survive he hijacks Mulder’s car. Scully tries to figure out if it’s a disease or something else causing the condition before the man dies or gets Mulder killed.
-Besides being just a generally good episode this one has the amusement of starting out as if it's a real new broadcast. It is quite convincing.
-Title notes: This is what the victim must do in order to survive; what he commands Mulder to do.
3) Triangle
Mulder boards a ghost ship in the Bermuda Triangle and is transported through time. He is pitted against WWII Nazis many of whom have familiar faces.
-I don't like episode that put the show's stars into other roles. It doesn't bother me quite so much with this one thanks to the great actors, the vastly different characters, and the humorous nods to who they look like. There's always the chance that this isn't real, anyway.
-Title notes: This takes places in the Bermuda Triangle
4) Dreamland
On the way to Area 51 to meet an informant Mulder finds himself in the body of a man in black. Morris Fletcher, an unscrupulous womanizer, has control of Mulder's body. Mulder will need to figure out who the real informant is and what is going on in order to get his life back. He's not cut out for the dysfunctional family life.
-This is a very odd but funny episode with a hysterical performance by Michael McKean.
-Title notes: Dreamland is the nickname for the area that is Groom Lake AKA Area 51.
5) Dreamland 2
Mulder has been named as the Area 51 informant, and since he is in the body of another man he can't turn to any of his normal sources of help. As he tries to convince Scully of what's going on in order to figure out how to put things right space-time disasters begin hitting all around him.
-Title notes: See the note for part 1.
6) How The Ghosts Stole Christmas
Mulder and Scully investigate a haunted house on Christmas Eve. The spooks want the agents to do each other in to gain more notoriety for their chosen haunt and begin messing with the pair's minds.
-This is one of the best spooky Christmas stories ever filmed. It's one of my favorite things to pull out during the yuletide season right alongside The Nightmare Before Christmas.
-Title notes: It's an obvious takeoff on "How the Grinch Stole Christmas."
7) Terms Of Endearment
A woman’s unborn baby is stolen by a demon. Mulder thinks the husband is the culprit, but other law officials say the evidence points to the mother being upset at finding out her baby would be born with deformities. The husband leads a second, secret life. He will try again to get what he wants.
-This is an odd take on demons in light of how we've seen them represented elsewhere in the series. It's not one of my favorite episodes despite guest starring Bruce Campbell.
-Title notes: “Terms of endearment” are used to display affection. Wayne uses them a lot with his wives. This is also the title of a movie. Though I've never seen it one summary says, “In the end, different people show their love in very different ways” which would very much apply to this story as well in a twisted sort of way.
8) Rain King
A small town and its surrounding areas are experiencing a terrible drought. Rain seems to follow a particular man who sells it for his personal gain. The area is known for its strange weather behavior which becomes dangerous for Mulder. Should he and Scully put a stop to the Rain King profiting from others' misfortunes? Is there anything they can do at all?
-Victoria Jackson guest stars.
-Title notes: Darrell is called the Rain King because the rain follows him.
9) SR819
Skinner may have been poisoned. Mulder and Scully race to uncover the plot against their former supervisor and save his life. They uncover a conspiracy linked to a senate resolution important enough to sacrifice not only Skinner's life, but the well being of other important men as well.
-Title notes: The senate resolution is number 819.
10) Tithonus
An old man takes pictures of the dead and dying. He’s being investigated because some of his photographs prove he was on the scene before police. Does he have something to do with the deaths? He’s definitely hiding something, and Scully is right in the middle of it.
-The explanation and resolution to this one are far fetched even for the X Files. I have a hard time buying the logic.
-Title notes: Tithonus is a mythological figure who was granted immortality but not eternal youth. So though he couldn't die, he did continue to age just like the old man in this episode.
11) 2 Fathers
Cassandra Spender is found in a train car with the bodies of burned scientists all around her. She is the first successful alien-human hybrid which means the alien invasion is slated to begin soon. Agent Spender faces off against his father and is introduced to a world of conspiracy with aliens. Will Spender become his father's dutiful replacement for Mulder?
-Title notes: This is a reference to Bill Mulder and CSM.
12) 1 Son
Cassandra is held in confinement under the guise of medical treatment. Colonization is imminent, but the vaccination work should allow the Syndicate to survive. Fowley and Mulder race towards the clandestine meeting while Spender makes a life-altering decision.
-Clear or not, this more or less explains the full scope of the conspiracy up to this point. Mulder gets some measure of vindication although it doesn't help a great deal.
-Title notes: This is a reference to Mulder.
13) Agua Mala
Some kind of water creature is causing people to disappear during a hurricane. Arthur Dales calls in Mulder to investigate. He's game, but Scully thinks it's a bad idea. When they are trapped in an apartment building with a deadly, unknown creature after them a bad idea gets worse.
-It's a fantastic monster story with a much enjoyed return of the older Agent Dales.
-Title notes: It means "bad water," but it's also slang for a dangerous type of jellyfish. The episode is all about a water monster which could be described as looking a bit like a jellyfish.
14) Monday
A woman is doomed to relive the day her boyfriend blows up a bank (with Mulder and Scully in it) until Mulder gets it right. As Mulder repeats the day over and over without any memory of the previous events the poor woman must find a way to convince him of what's going on.
-It's Groundhog Day X Files style. There's a nod to the Dreamland episode. Not everything went back to normal.
-Title notes: It's a reference to the day that's being repeated.
15) Arcadia
Mulder & Scully go undercover as a couple buying a house to investigate the disappearances of families in a planned community. The people here seem friendly and helpful, but something sinister is going on.
-This is a good mix of humor, intrigue, and good old monster mayhem.
-Title notes: This is the name of the community (The Falls at Arcadia) which itself is a reference to the Grecian region of ideal peacefulness.
16) Alpha
Evidence points to a rare dog killing people except that it seems to be able to open and close doors and have a human-level intelligence. Mulder seeks help from an animal behaviorist who may have an ulterior motive. Scully doesn't trust her, but Mulder acts like he has finally found a kindred spirit.
-While I like the character moments with Mulder and his new friend, the supernatural part of the story falls flat.
-Title notes: The villain behaves as an alpha male.
17) Trevor
A prison inmate gains the ability to pass through solid objects. Now he’s looking for his ex-girlfriend who stole something he wants back more than anything. The X agents are the only hope for stopping him.
-Title notes: This is the name of the boy that is at the center of attention.
18) Milagro
A writer is obsessed with Scully and follows her around. Meanwhile people are killed by having their hearts removed without any mark or incision. To make the case stranger the writer seems to be writing those events in his novel with incredible accuracy. What is his involvement, and what does he have in mind for Scully?
-This one tries to go for a more poetic story. There is a lot of metaphor and vague plotting here. It's not a favorite of mine.
-Title notes: It means “miracle” and is what the charm that Scully is given is called.
19) The Unnatural
Mulder finds a strange picture which sends him looking for Arthur Dales once more. It turns out to be Arthur’s brother who had a strange experience with an alien posing as a baseball player. Mulder wants to hear the man's story.
-Title notes: It's a pop culture reference drawing attention to the fact that the hero is not natural by earthly standards.
20) 3 Of A Kind
The Lone Gunmen discover a conspiracy at a comic convention. There is a drug that makes people very susceptible to suggestion. Byers runs into his old girlfriend Suzanne, very much alive, who may be involved with the creation of the drug. They pull in Scully and get themselves in the crosshairs of some dangerous people.
-Title notes: This is a poker term applied to the Lone Gunmen.
21) Field Trip
Hikers go missing for a couple of days to have their skeletal remains turn up in a field. They haven’t had time to decompose, and they haven’t been eaten. Are aliens placing false skeletons to cover up abductions? When Scully finds Mulder's body the quest is on to find the killer except that she seems to be the only one suspecting foul play.
-This is a very surreal episode.
-Title notes: Much of it takes place in a field and it involves a sort of drug trip.
22) Biogenesis
Strange relics are found leading to an alien spacecraft that has been grounded and mostly buried. Mulder seems to be losing his mind, and Scully can’t deny the existence of the “flying saucer.”
-This introduces the new mythology.
-Title notes: The inscriptions found on the ship suggest that it holds the answer to the origins of biology.