Picking these were a lot easier than the ten best, since they were few and far between on such a high quality series. However, a few did slip by:
Mulder and Scully, searching for a group of missing loggers, learn that a nest of tiny bugs has been accidentally released, which promptly begins to kill everyone in sight. However, there are so many plot holes in this episode that it insults the viewer's intelligence. How do tiny bugs manage to cocoon a full-grown man inside a tree? Mulder allows an eco-terrorist to leave the area with the only working vehicle, effectively stranding them. If the bugs are afraid of light, why don't Mulder and Scully build a fire in the cabin they're hiding out in?
In Chris Carter's least favorite episode of the first season, something is sabotaging the space shuttle. Mulder and Scully get sent to investigate and find that the man in charge of the space shuttle mission, Lt. Col. Belt, is under the influence of an alien presence somehow related to the 'face' on Mars (?). The story shows signs of being rushed with its logical inconsistencies. For example, at the end of the episode, an alien presence is onboard a shuttle reentering the atmosphere causing all sorts of problems, and it is only by altering the reentry trajectory of the shuttle that this presence is neutralized, which is about as logical as the old comic book convention of 'reversing polarity' to blow something up. Throw in some lackluster special effects and not actually 'seeing' what's happening on the space shuttle, and you have one bad X-Files episode.
Mulder and Scully investigate a Navy ship caught in an area of the Norwegian Sea where everything ages rapidly due to a high level of free radicals in the sea water. Now if you can believe that, then the ending should make perfect sense to you, when Mulder and Scully, almost dead and having aged in excess of fifty years, return to their normal soft and pink selves in no time. Syeah, right. At least on Star Trek, they use the transporter buffers to get away with this stuff.
The fifth episode of the series came off the strong momentum from the pilot episode, "Deep Throat", "Squeeze", and "Conduit", and kicked off a three-episode low point that caused a lot of viewers to lose interest (including me-- I didn't start watching again until "Beyond the Sea"). This silly episode had Mulder and Scully find a Bigfoot-like creature lurking around New Jersey that has been giving birth to little beast-babies. About the only thing of interest that happens in this episode is that Scully goes on her one and only date (until "Betty").
This premise of the 'sick building syndrome' has been done to death over the years from "2001: A Space Odyssey" to The New Avengers (remember that one?) to some cheap made-for-TV movie on Hamilton's CHCH. The Central Operating System, which controls everything in a high-tech office complex, goes nuts and starts killing anyone that tries to alter its programming. Unfortunately, COS had no personality-- just blinking lights that reacted. Yawn.
Mulder and Scully investigate a series of killings, both men and women, and they find that the killer is part of a group called the Kindred who can change genders and teleport (!). It ends with Mulder and Scully finding a crop circle, implying that they are extraterrestrials (Amish from outer space!). This episode also has an embarrassing moment for Scully, where she is almost hypnotized into doing the nasty with one of the Kindred.
This Scully-less episode existed only because Gillian Anderson was on maternity leave. The story, which gets really confusing at times, follows Mulder to Los Angeles where he investigates a series of murders where the perpetrators have drank the victim's blood. He behaves uncharacteristically stupid when he becomes romantically involved with a woman (Perrey Reeves, Duchovny's girlfriend at the time) who may or may not be one of the killers and allows her to give him a shave. If you watch this episode, only watch the first couple of minutes, when Mulder is in his office and looks at the X-File set up for Scully's abduction.
Killer pussycats? What will they think of next? A sacred urn is removed from a South American burial site and taken to a Boston Museum. When people begin dying, Mulder and Scully get called in. I was really scared when Mulder and Scully were in the sewers and all those kitties were after them.
When I heard about this episode, I thought "cool, the X-Files will do an involved examination of the multi-faceted Chinese culture". In this cliché-ridden episode (which probably would have been at home on any cop show), Mulder and Scully uncover an illegal organization that gets black-market body parts from willing donors ready to gamble. I have never heard so much mangled Cantonese spoken on a television show (even worse than "Kung Fu: The Legend Continues"). The Chinese Cigarette-Smoking Man (James Hong) was kind of interesting though.
The third season finale was disappointing. Basically it said a lot of things, but didn't tell you anything (case in point, the long cryptic conversations between Jeremiah Smith and Cigarette Smoking Man). And the almost anti-climactic ending, with the Bounty Hunter walking slowly towards Mulder and Scully, certainly lacked the punch of the other season finales (Deep Throat being killed and the X-Files being closed in season one and Mulder in a burning train car in season two).
And let us just pray that they never do a 'clips' show (Mulder and Scully sitting around the office late one night, drinking coffee and reminiscing about the cases they've worked on; "Scully, remember the time..."; wavy dissolve; show clip).