The second season of the X-Files really starts to pick up. Character development is excellent, and the story lines are strong. Season 2 is so strong, in fact, that I’m putting more than half of the episodes in the “must see”.
2×01: Little Green Men
Season 2 opens on a good foot. With Mulder and Scully separated, and the X-Files shut down, Scully convinces Mulder to carry on his search for the Truth. Mulder takes her suggestion when a congressman passes him a print out of a strange transmission.
2×02: The Host
Okay, this is a must-see mainly because the villain is amongst the most ludicrous of all X-Files villains. Additionally, he/she/it is mentioned by Scully in a later episode.
An X-Files government conspiracy mystery that plays science, war, and the world of dreams off of each other. However, more importantly, this episode marks the first appearances of Mr. X and Alex Krycek, and sets things up for the next phase of the overall arc of the X-Files “mythology.” The episode also features Jonathan Gries, whom some may know as Roger Linus from __Lost__, or Uncle Rico from __Napoleon Dynamite__ — the really awesome people will know him as Lazlo Hollyfeld in __Real Genius__.
2×05: Duane Barry (I)
Still separated, Mulder gets himself wrapped up in a hostage negotiation with an ex-FBI agent, Duane Barry, who claims to have been abducted by aliens. Scully gets roped into the action when she discovers that Duane Barry may be telling the truth.
2×06: Ascension (II)
After Scully’s abduction by Duane Barry, Mulder and Krycek disobey orders to try and find them. But Krycek’s collusion with the Smoking Man takes on a whole new level of wickedness. Really, this episode just makes you ask: “What the heck is going on?” Luckily, we see a light at the end of the tunnel…
2×08: One Breath
Possibly my favorite overall episode. This tale, which begins with Scully’s body showing up in a hospital, traces Mulder’s fight to find the truth behind her abduction, and Scully’s fight to stay alive. More than anything, this episode showcases the growing relationship between our intrepid special agents.
2×10: Red Museum
Bradley Whitford fans will no doubt be upset that I’m skipping over Firewalker. While it’s definitely a good episode, I think it’s best to move on with the conspiracy. Red Museum does just that. Hearkening back to the end of Season 1, this episode features Mulder and Scully in the middle of nowhere, yet deep in the conspiracy as they find what may be “Purity Control.”
I’ve always liked this episode. It doesn’t hurt that this is the first of Terry O’Quinn’s three X-Files guest roles — the LOST star plays three different characters in three different X-Files stories! Here he’s a detective in a rural town, Aubrey, Missouri, where a series of murders are taking place. Mulder and Scully arrive on the scene because a 50-year-old corpse has been found which may match the recent murders.
Creepy! Not only is Donnie Pfaster one of the creepier X-Files villains, but in this episode we also get a look at Scully’s fears. Strong episode that really helps us get to know Scully.
2×16: Colony (I)
A good conspiracy episode. Mulder and Scully investigate the deaths of abortion doctors that appear to be identical. Meanwhile, they are befriended by a CIA agent who may not be all that he claims to be. Several twists along the way to the cliffhanger finish including the return of Mulder’s sister, Samantha.
2×17: End Game (II)
With Scully taken captive, Mulder is forced to decide whether to abandon her or give up his sister in exchange. After making the exchange, Mulder travels North in search of his sister and answers with renewed hope for his quest.
This episode is just ridiculous and fun(ny). Mulder and Scully find themselves investigating a series of strange murders in Gibsontown, Florida — a place mostly inhabited by circus sideshows, “freaks” if you will.
2×22: F. Emasculata
I had forgotten how intense this episode is. Two convicts are on the lam and may be infected with a deadly toxin that kills within 36 hours. While Scully must stay behind, quarantined because she may be infected, Mulder hunts down the escapees and the pharmaceutical company conspiracy behind the epidemic.
2×23: Soft Light
Tony Shalhoub guest stars as a scientist whose experiments have gone terribly awry. For me, this is just a good, solid episode, punctuated by an interesting turn: X betrays Mulder and Scully.
2×25: The Anasazi (I)
One of the best X-Files conspiracy episodes, and an extremely memorable season finale. Mulder, for reasons unknown to him and Scully, begins acting erratically. Meanwhile, the Lone Gunmen set Mulder up with a hacker who has wormed his way into the Department of Defense’s computer system and found some very intriguing files, encrypted in Navajo. Mulder and Scully’s search for the meaning of these files takes them into the New Mexico desert where Mulder’s life hangs in the balance.