- The season 1 finale "The Erlenmeyer Flask" set the wham standard for all subsequent season finales. We see the first alien-human hybrid, Scully receives near-indisputable evidence of extra-terrestrial life, Deep Throat is shot dead, and the X-Files unit is shut down (for the first time).
- The three-parter consisting of season 2 finale/season 3 première and season 3 second episode, containing the episodes "Anasazi", "The Blessing Way" and "Paper Clip", is pretty big. Mulder and Scully are pursued by a hit squad, Mulder is presumed dead (for the first time in the series) and Scully is on suspension. By the end of "Paper Clip", Mulder's father and Scully's sister are both dead.
- "Leonard Betts" starts off as an investigation into a man with a Healing Factor who fuels it by consuming cancerous tissue, usually killing the person he's extracting it from. Standard for a monster of the week episode. Then, at the climax, he turns to Scully, of all people, and says, "I'm sorry, I'm so very sorry... but you have something I need."
- "Musings of a Cigarette Smoking Man". The episode is remembered for being CSM's A Day in the Limelight and revealing much about his past through a lengthy flashback that many took as gospel. However, Word of God has reminded fans that the supposed backstory comes from a conspiracy theory magazine article that is implied in episode to facilitate an Unreliable Narrator.
- "Christmas Carol"/"Emily," in Season 5, where Scully discovers that she has a biological daughter who is an alien-human hybrid and the daughter subsequently dies. This all happens shortly after Scully is told that, due to procedures done during her abduction, she cannot have children.
- Season 5 finale "The End", which ends with the X Files department being closed down and Mulder's office (including all the files) being burned to the ground.
- Season 6's "Two Fathers/One Son" sees the destruction of the Syndicate and the apparent death of Jeffrey Spender.
- "Closure," in Season 7, where the portion of the Myth Arc regarding Mulder's sister is concluded. She really was abducted by the conspirators collaborating with aliens and suffered horribly as they were performing tests on her. Then she lived with the Spenders, AKA The Cancer Man's family, who may or may not be the Mulder siblings' biological father. When she was fourteen, she was taken by some weird types of angels or fairies who saved her. This means her body can never be found, or something, but Mulder did see her ghost.
- "all things" in season 7, in which Mulder and Scully finally relieve all that UST. Not a wham episode in the traditional sense, since it actually didn't change Mulder and Scully's onscreen relationship as much as you think it would. However, it is heavily implied that this episode marks the start of their Relationship Upgrade and they were together, but hiding it.
- Season 7 finale "Requiem" is very big. Mulder is abducted by aliens, marking the beginning of his absence on the show to the first two thirds of the following season. Scully, who can't have children becuase of her abduction, finds out she's pregnant.
- "Per Manum" was an episode full of "wham" moments, from the revelation that Mulder told Scully he'd found her ova, to her going through with IVF to Mulder agreeing to be the father of her child and then the IVF failing. WHAM!
- The two-part Season 8 finale, "Essence" and "Existence" is wham-esque. Scully's baby is born, ending her official assignment to the X-Files, and Krycek is finally killed.
- "William" in Season 9, which involves the revelation that Scully's son is a super soldier and ends with Scully giving him up for adoption to keep him safe.
- "My Struggle", the opening episode of the miniseries. Mulder and Scully have broken up since I Want To Believe. After coming out of near-seclusion, Mulder begins to form a new conspiracy that the alien colonization was a smokescreen for a takeover plan by human elites. The X-Files are re-opened after more than a decade, and the Cigarette-Smoking Man is shown to be alive.
- "My Struggle II", the concluding episode of the miniseries and the continuation of "My Struggle". People around the world start falling ill and dying from complete immune system failures, an event orchestrated by the Cigarette-Smoking Man. It turns out that Monica Reyes cared for CSM after his presumed death. Mulder falls ill while confronting CSM and turns down an offer to be given the alien DNA that will make him immune — the same DNA Scully has, which is the only viable cure for the disease. Scully finally finds Mulder in a crowded overpass, but realizes that he's so near death that the DNA will not be enough to help him; the only cure has something to do with William. And just as this comes to light, the same UFO that blew up a woman's car in "My Struggle" appears right above the overpass, preparing to strike.
Wham Episode / The X-Files
The X-Files pulls Wham Episodes very often. The seasons' last episodes, ending with cliffhangers and deaths of major characters, or two-parters and trilogies which usually uncovered new bits of the series' Myth Arc.