These are not the best episodes, but the ones most important for catching up with the X-Files mythology.
With The X-Files revival, I figure people are going to start watching the series to catch up. It's a long series with a complicated plot, and only some of the episodes are about that plot. So for those wanting to rewatch the show but not sift through the entire series, these are the essential episodes of The X-Files.
The first movie takes place between seasons five and six is and important. The second movie takes place after the series.
The complete extraterrestrial story lines and related conspiracies of THE X-FILES per Wikipedia, which combined information from series DVDs with information from the book entitled THE COMPLETE X-FILES: BEHIND THE SERIES, THE MYTHS AND THE MOVIES. Episodes included in only one of the two sources are still included here. Also included is the first feature film.
List of episodes I've watched in 2019.
New shows started: 24
→ Murder Mountain, Tidying Up with Marie Kondo, Sex Education, Planet Earth, RuPaul's Drag Race All Stars, Selviytyjät Suomi, The Umbrella Academy, Sick Note, Modern Family, Love, Death & Robots, After Life, Black Mirror, You ws. Wild, Tuca & Bertie, Chernobyl, Titans, Car SOS, RuPaul's Drag Race: Untucked!, Conversations with a Killer: The Ted Bundy Tapes, The Spy, Happy!, Shooter, How I Met Your Mother, Dirk Gently's Holistic Detective Agency
Shows completed: 15
→ Star Trek: The Next Generation, Marvel's The Punisher, Unbreakable Kimmy Schmidt, The X-Files, Bates Motel, Game of Thrones, New Girl, Tuca & Bertie, The Americans, Chernobyl, Orange is the New Black, Conversations with a Killer: The Ted Bundy Tapes, The Spy, Happy! , Shooter
New episodes: 974
Rewatched episodes: 8
Murder Mountain S1E01
Bob's Burgers S8
American Crime Story S2
Chilling Adventures of Sabrina S1E11→S1E12
Tidying Up with Marie Kondo S1
Star Trek: The Next Generation S6E23→S7
RuPaul's Drag Race S10E04→S11, S1
Sex Education S1
BoJack Horseman S5
Marvel's The Punisher S2
True Detective S3
Star Trek: Discovery S2E01→S2E05
DC's Legends of Tomorrow S3E11→S4, S2E07, S3E08
Unbreakable Kimmy Schmidt S4
The Last Man on Earth S3E01→S3E03
The X-Files S8E06→S11
Selviytyjät Suomi S3E01
Planet Earth S1E01→S1E10
Arrow S6E13→S6E23, S5E08, S6E08
RuPaul's Drag Race All Stars S1→S2E08
The Flash S3→S4
The Umbrella Academy S1E01→S1E04
Sick Note S1E01
Modern Family S1→S9
Love, Death & Robots S1
Bates Motel S5
Game of Thrones S8
After Life S1
Black Mirror S1→S5, Special 1
You vs. Wild S1E01
New Girl S7
Tuca & Bertie S1
Nailed It! S3
The Walking Dead S8
The Americans S6
American Horror Story S7
Car SOS S2E01→S2E04
How to Get Away with Murder S4
Stranger Things S3
Queer Eye S3→S4
Orange is the New Black S6→S7
RuPaul's Drag Race: Untucked! S11
Peaky Blinders S5
Conversations with a Killer: The Ted Bundy Tapes S1
The Spy S1
Brooklyn Nine-Nine S5
Big Mouth S3
How I Met Your Mother S1E01→S1E02
Dirk Gently's Holistic Detective Agency S1E01→S1E02
The Mytharc is the overarching story developed in a series of episodes of The X-Files where Mulder and Scully investigate and expose an international conspiracy by an organization known as the Syndicate to develop a human/alien hybrid and suppress knowledge of the existence of extraterrestrials who plan to colonize Earth.
It should be noted that some key mythology characters also appear in Monster of the Week episodes; notably, Deep Throat, X and the Cigarette Smoking Man each appear in episodes which involve government activities.
Furthermore, as his role expanded, Walter Skinner appears in more Monster of the Week episodes.