The third season is probably not as good as the second, especially in terms of writing. However, __The X-Files__ budget continued to grow; therefore, the third season gives many great episodes and with very high production quality. Here are my favorites:
3×01: The Blessing Way (II)
With Mulder’s life hanging in the balance, Scully is at a loss as to where to turn. This episode, a continuation of the season 2 finale “The Anasazi”, is a great way to start off season 3.
3×02: Paper Clip (III)
Thanks to a very speedy recovery, Mulder is now able to assist Scully in their quest to discover the truth. Mulder finds a photo that features his father and some very curious individuals from a post-WWII era science project known as “Operation Paper Clip.” Where this leads our agents is quite a surprise, and in West Virginia of all places!
3×04: Clyde Bruckman’s Final Repose
This episode guest stars the late, great Peter Boyle (who won an Emmy for his performance here), as Clyde Bruckman — an insurance salesman who reluctantly possesses psychic powers. Truly a tender episode with its fair share of pathos.
Mulder takes a case in which a woman who was kidnapped 20 years ago seems to have some psychic link with a recent kidnap victim. This is one of those great episodes where we really see Mulder and Scully get at each other. Scully is concerned that Mulder has grown too close to the victim; so close that it’s blinding his judgment.
3×09: Nisei (I)
The first part in another two-part conspiracy episode starts off with Mulder purchasing an alien autopsy video (“Not [his] usual form of entertainment” as Scully says). Of course, this is a comical premise since FOX was running its own alien autopsy video at the same time. As they investigate, however, they find an international conspiracy as well as some disturbing news about the implant in Scully’s neck.
3×10: 731 (II)
In hopes of finding proof of alien existence, Mulder ends up locked in a railroad car with a killer and a bomb. Meanwhile, Scully has found evidence of a conspiracy in which the US Government was using humans as test subjects. She is given a great deal of help and information from a conspiracy member known as “The Elder.”
In spite of a terrible child acting performance (I’m sorry, but it’s just dreadful), this episode gets my seal of approval thanks to more insight into Dana Scully’s faith. When Mulder and Scully track down a man who is murdering stigmatics, Scully begins to wonder if she has been chosen by God to protect the one true prophet in the group.
3×12: War of the Coprophages
If you like Mulder and Scully being somewhat flirty/cutesy, and a storyline that constantly makes fun of the X-Files — here’s your episode!
This is not a great X-File, but it is a lot of fun to see Mulder and Scully get snippy with each other as the universe’s negative energy reaches a peak.
I particularly enjoy this episode because of Mulder’s obsession. Occasionally, in the X-Files, you get an episode that really focuses on Mulder or Scully. In this case we get a lot of good character info about Mulder as he tries to track down a copycat killer who may be possessed.
3×15: Piper Maru (I)
This first part of a two-parter is hugely important in the X-Files conspiracy canon. When a French ship attempts to recover some World War II wreckage in the Pacific, an evil force is unleashed. Here we have the first appearance of the famed black oil!
3×16: Apocrypha (II)
As Mulder and Scully continue to investigate the mysterious illnesses that have occurred in conjunction with the World War II wreckage previously mentioned, the government conspirators attempt to block their access.
Oh my! Robert Modell has one of the more devastating paranormal powers. Known as “Pusher” he is able to force his will on others in a unique and deadly way. When he forces Mulder to turn on Scully, things get particularly interesting. This episode has one of my favorite endings of any X-File.
3×20: Jose Chung’s ‘From Outer Space’
A great comedy episode guest starring none other than Jesse Ventura and Alex Trebek! Must see.
Scully’s paranoia reaches a fever pitch as she and Mulder investigate a rash of killings by normal suburbanites which may have been triggered by secret government experiments. Watching Scully turn on Mulder over the course of this episode is suspenseful and heartbreaking.
3×24: Talitha Cumi (I)
“Talitha Cumi” has always been one of my favorite season enders. An older gentleman, Jeremiah Smith, appears to possess miraculous powers. When these powers draw attention to him, the agents are drawn once again into the government conspiracy which hits a little too close to home for Mulder.