The second season of X Files includes 25 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) Little Green Men
Have we made contact with aliens through Voyager? Hmmm….. Mulder and Scully are on their separate assignments, and Mulder is taking the separation pretty hard even to the point of developing doubts about what he once believed so strongly. A Senatorial ally points him to possible proof of contact. What will he risk to get his evidence?
-Title notes: It's a popular description of aliens – Mulder’s reference to what may be his delusion.
2) The Host
Something is living in the sewers and attacking people. Who better to investigate than Mulder? He’s reluctant at first but starts changing his tune when the attacker proves monstrous in the truest sense of the word. X approaches with a bit of help and Skinner shows signs of not being the enemy Mulder assumes.
-I hear more mixed reviews of this one than most any other episode. Some love it while some find it unbearably hokey. I’m somewhere in the middle. I can see why it’s too much for some, but I can’t help but enjoy it even if it’s not my favorite.
-Title notes: It's a reference to the parasitic nature of the monster.
3) Blood
Computers and other machines are driving people to kill by giving them murderous commands. An evil AI, possession, or chemical induction? Mulder sets out on a late night expedition to find out. What he uncovers is even more chilling than the crimes he’s investigating.
-William Sanderson guest stars.
-Title note: This is the phobia of one of the would-be killers.
4) Sleepless
People are dying, but the cause seems to be all in their minds. A man with control over the dream world is taking revenge for the experiments done on him. Mulder has to wrestle for the case with the current assigned agent, an ambitious young man named Alex Krycek. The Syndicate and X are brought fully to the viewer’s attention.
-Tony Todd guest stars.
-Title notes: The “monster” of the week can’t sleep.
5) Duane Barry
Duane is a regular abductee, and he’s paranoid that the aliens are coming back for him. In a bid to get attention he takes a group of hostages. Mulder is called into the negotiations to talk as one believer to another. When Duane starts giving hints of the Syndicate’s involvement with the aliens and ties to Mulder’s sister, Mulder takes notice of him in a different way.
-Title notes: It's the name of the man that’s the focus of the episode.
6) Ascension
Picking up where we left off last episode Duane is on the lamb and kidnaps Scully. He is taking her to his abduction site to offer a trade: her life for his. Mulder and Krycek are partnered once again, but the latter begins showing his true nature.
-The results of this episode are really the kickoff for the interconnectivity of the ongoing mythology storyline.
-Title notes: Duane believes he will ascend to the stars.
7) 3
Mulder is still reeling from Scully’s disappearance, but he’s at least back on the X Files. He wastes no time getting back to work investigating a series of vampiric-like murders. The question is are the culprits really vampires or just delusional? He comes across a beautiful suspect. Convinced she’s in danger he stays to protect her, but he may be the one needing protection.
-This is a slow but enjoyably moody episode. The piano score is particularly nice. Scully is no longer a part of the show marking the beginning of a narrative that is ever changing rather than stories that begin and end in the same place.
-Title notes: This is a reference to the trinity the vampires see themselves as.
8) One Breath
It’s time to declare Scully presumed dead. Suddenly she shows up in the hospital though for all intents and purposes she’s gone – alive only with the help of machines. Mulder sets out on a quest to find evidence of the experiments he’s sure were conducted on her. It’s a race against time as Scully’s time dwindles away, but Mulder will go to any lengths to save her, even confront the Devil himself.
-Title notes: It's a reference to the thin line between life and death and is taken from dialogue in the episode.
9) Firewalker
Something happens at a volcano research camp and the newly reunited team of Mulder and Scully are called upon. When the agents arrive they find the facility in shambles and a man scared to death of the project leader. Could a new and dangerous life form be at work here? The agents better find out quickly before everybody dies.
-Shawnee Smith guest stars.
-Title notes: This is a dual reference to the name of the research robot and the possible new life form.
10) Red Museum
A boy in a quiet little town gets a mysterious phone call and hours later turns up naked and disoriented in the woods. Alien abduction? The sheriff suspects a strange vegetarian cult. Others blame cow growth hormones. The X agents’ best lead is a weird peeping tom. Thinking the case is over, the stakes are suddenly raised when people, including the sheriff’s son, are executed. Mulder becomes desperate for answers when links to Purity Control (see "The Erlenmeyer Flask") and the demise of Deep Throat are uncovered.
-Mark Rolston guest stars.
-Title notes: It's the name of the cult.
11) Excelsis Dei
Something strange is happening in the room of a dead woman – a nurse is raped by an invisible force. There’s virtually no evidence but since when did Mulder need any of that to investigate a case? The problem is that the suspects keep dying. Could the spirits of the deceased residents of the assisted living facility be hanging around?
-This one is weak in the narrative department. The ending in particular has some dangling threads I would like to have seen tied up more neatly. Despite its shortcoming it’s still an entertaining episode, though.
-Teryl Rothery (another SG1 favorite) has a small role.
-Title notes: It's the name of the facility where the events take place.
12) Aubrey
A woman has a strange vision and finds herself digging up the skeleton of a presumably murdered FBI agent. The victim was a pioneer in catching a particular serial killer who appears to be back on the job. The current investigator’s dreams seem to be the best link to what’s happening.
-This is probably the weakest story in this season. The whole concept is weak and the significance of “sister” and needing someone to blame aren’t sufficiently connected.
-Title notes: This is where the events take place.
13) Irresistible
The agents are investigating Donnie Pfaster, a supremely creepy man that likes defacing corpses. Mulder is worried that he will advance to creating corpses. Not only is he too late to stop Donnie, Scully has made the list of his corpses to be.
-Wow. After the previous weak episode what a one to follow up with. Highly disturbing, Donnie is one of the creepiest human characters in the run of X Files.
-Jesse Martin plays a small role. He will come back later to play a different, much larger role.
-Title notes: It's a reference to the killer’s fetish – he finds women irresistible.
14) Die Hand Die Verletzt
The local school board is praying to demonic forces. Some of the local kids try their hand at black magic and end up finding themselves murdered. But if the local cult didn’t do it who did? Could a demon have actually been called up? Mulder and Scully are in very dangerous territory as they have been targeted by dark forces, but they are determined to unravel the secrets of this hellish town before more people die.
-We’ve now more than made up for the earlier weak episodes. This one is a classic, one of my favorites of the entire series and is a favored annual Halloween viewing experience.
-Title notes: The translation is “the hand that wounds;” it is part of the demonic prayer uttered by the cult.
15) Fresh Bones
Jack, a devoted husband and soldier, is freaking out and in a hysterical fit dies in a car wreck. His wife thinks murder although nobody else does. That’s good enough for Mulder and when he and Scully begin investigating they become the targets of dark attacks. When zombies start walking the streets they know something is definitely going on that defies easy scientific explanation.
-Title notes: Bones fresh out of the cemetery are the best for voodoo rituals.
16) Colony
Mulder’s sister appears out of the blue claiming she’s in grave danger. She’s being hunted by a bounty hunter that has been killing a number of men who look exactly the same. A Russian plan gone awry? Aliens? You’ll have to wait until next week to find out.
-Title notes: It's a reference to the group of identical people being hunted – Mulder thinks they are looking for a Russian colony though it turns out to be something quite different.
17) End Game
Picking up where we left off last time, Scully has been taken by the bounty hunter. Samantha tells a story of alien colonization and genetic experiments to help them blend in. The bounty hunter is supposedly cleansing the population. But how much of her story can truly be trusted? Emotions run high when Mulder must decide between Scully and his newly rediscovered sister. Emotionally distraught to the point of insanity Mulder chases a bounty hunter he knows he can’t kill to a stranded submarine in the Antarctic.
-While indicative of the kinds of episodes that provide information you don’t know if you can trust and that leave Mulder maddeningly at square one each and every time, these two episodes are great and are the first real building block to the vast conspiracy that is starting to unfold.
-Title notes: This is a reference to the confrontation that nearly kills Mulder, they have reached the end of the game.
18) Fearful Symmetry
A powerful, invisible force wreaks havoc in the city. Somehow zoo animals are getting loose and running amuck while invisible to the naked eye, Aliens or the work of an animal rights organization with a powerful secret? The best witness is a gorilla. Interrogation is going to be interesting.
-Title notes: This references a poem about wild animals and their fierceness.
19) Dod Kalm
A ship’s crew is abandoning their vessel much to the chagrin of the captain. When the crew shows up on land vastly aged Mulder expects experiments with time. He travels to investigate and ends up stranded on a ghost ship aged far beyond its actual years. What’s worse is that someone is killing the people he has brought with him one by one. He and Scully begin aging rapidly – desperately trying to figure out what’s happening before they die of old age.
-Title notes: It's a Norwegian-esque use of “dead calm” – which is s phrase used for remaining unmoving at sea.
20) Humbug
When a “circus freak” is murdered Mulder and Scully investigate. They end up in a town full of unusual people – sideshow performers. Who’s a suspect? The shady guy that feels no pain? The one that eats live animals? Who’s really a viable suspect and who is suspicious just because they’re weird?
-Title notes: A “lie” - where does the truth end and the humbug begin?
21) The Calusari
Mulder and Scully investigate the seemingly supernatural death of a toddler but come to suspect the involvement of human forces when they find the child’s grandmother involved in strange rituals. Now the other child of the family may be in danger from these Romanian rites, but the participants claim it is an exorcism ritual.
-Title notes: This is the group that oversees the correct observance of the sacred rites.
22) F Emasculata
Some kind of infection is spreading and killing without discrimination. Mulder and Scully are sent to work detail on two escaped convicts who may be carriers. Now the agents may be exposed, too. Scully finds a secret CDC quarantine in effect, but despite the danger they are not forthcoming about the situation. Just what all does the govt. know about this?
-Title notes: It's the name of the bug that carries the parasite.
23) Soft Light
A man unwittingly dissolves people with his shadow. He tries to avoid it, but a mishap puts Mulder and Scully on his trail. With others of less integrity also after him the killer is afraid if he dies his shadow will become basically a murderous free-agent. X gets involved and finds that even he is in over his head. What’s more, his actions put him at moral odds with Mulder.
-Tony Shalhoub guest stars.
-Title notes: It's what the “monster” needs in order to keep from casting his dangerous shadow.
24) Our Town
When a man disappears in the woods Mulder suspects Indian spirits. When they discover he was at odds with the chicken plant that is the lifeblood of the town suspicions take a more natural turn. When a woman from the town dies Scully’s autopsy proves that she is much older than seems possible. If there weren’t enough questions defying explanation, several people in the town develop the same extremely rare disease. When Mulder and Scully start poking around the graveyard the townsfolk realize that in order to keep their secrets they must get rid of the agents by any means necessary.
-This is one of the most disgusting and even disturbing episodes ever. Some people quit watching the show altogether after this. Despite its subject matter, though, it is a well done and highly suspenseful episode.
-Title notes: It's probably inspired by the famous play. It is spoken by one of the townsfolk referencing the town conspiracy.
25) Anasazi
An earthquake reveals a buried secret – a train car full of corpses that appear to be alien. Meanwhile a hacker steals evidence from the D.O.D. proving that the govt. knows about the existence of aliens. The Lone Gunmen get involved and turn to Mulder. Our resident hero agent is acting even more paranoid than usual these days even to the point of attacking Skinner. When his dad is murdered he is the prime suspect, and his road to vengeance against the most likely culprit, Krycek, puts him at odds with Scully. Trying to sort through all this mess and keep the hacked information out of the wrong hands while trying to decipher it the agents are set after by CSM whose ruthlessness comes out in full force.
-Title notes: It means “ancient aliens.” It’s a reference to a real group of people that disappeared many years ago. Some believe they were abducted.