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The Sixth Extinction II: Amor Fati
Scully: Well, whatever it is, it's killing him. And we have to get it out of him.
Mulder is taken from the hospital by the Cigarette Smoking Man, who offers him a new life free from the pressures of fighting the alien colonizers. Meanwhile Scully and Michael Kritschgau seek answers about what has happened to him and his alien condition.
- Adventures in Comaland: While in a coma, Mulder dreams he is led by CSM to a simpler life, where lives in a suburban neighborhood, is married to Diana, has children, and his sister is alive with children of her own. He leaves behind his quest, and the sequence ends with CSM comforting Mulder in his deathbed, curtains hiding the alien invasion happening outside.
- Affectionate Gesture to the Head: Mulder and Scully hold each other's faces in his doorway, and Scully touches his lips as well.
- All Just a Dream: Mulder's idyllic world with Diana? It's nothing more than a coma dream while he is undergoing brain surgery with the Cigarette Smoking Man.
- Anywhere but Their Lips: Scully to Mulder, which is pretty much the longest forehead kiss in history.
- Artistic License Medicine: Mulder and CSM have brain surgery, but no shaved heads. Mulder only has a piece of gauze around the middle of his head a week later, with a full head of hair around it.
- Bookends: For the entire three-parter. In "Biogenesis", the final bird's-eye shot was that of Scully witnessing the alien spaceship submerged underwater, beginning her contemplation of her scientific mindset. Here, the episode ends with another aerial zoom-out, only this time, it's Mulder's dream of him and a boy building that spaceship out of sand with the ocean on their right. This affirms Mulder's return to uncover the truth, as he has already imagined what it would be like if he gave up his crusade.
- Call-Back: CSM's commentary on what men whose destiny is to affect the world truly desire from it ties back into his Villain Episode three seasons prior, which offered an interpretation of his character as a lonely man welded to his job, whose real passion in life is much more humble than heading up a global conspiracy.
- A Death in the Limelight: Mimi Rogers as Diana Fowley gets a lot more to do in this episode than usual, and then Fowley is killed off at the end. In the DVD commentary, Rogers says that when she was reading the script for the first time, she realized partway through that it was going to end with her death because of this trope.
- Dream Within a Dream: Mulder has one of himself and a young boy on the beach building a spaceship while living out his alternate life in his coma.
- Fairy Tale Motifs: "The Snow Queen".
- Friend-or-Idol Decision: Mulder has to choose between saving Scully and finding the truth about the alien conspiracy.
- HeelFace Turn: A bit of one for Diana, who leaves Scully a clue that leads to Mulder's location which costs her her life.
- Held Gaze: Mulder and Scully at his door, during and after the "my constant, my touchstone" conversation.
- Jerkass Has a Point: Scully is scathing towards Kritschgau for 'shooting up' Mulder with a drug he requested, while Kritschgau rightly points out it was Mulder who wanted his involvement and help in the first place. To bring to light what has happened to Mulder. Despite his coarse personality, he makes a number of good points in the episode like he did in the last, for all the good it does him.
- Killed Off for Real: Michael Kritschgau is murdered by Krycek for his alien data, Diana Fowley is murdered on CSM's orders for her betrayal, and Albert Hosteen passes away from his illness.
- Luke, I Am Your Father: The Cigarette Smoking Man outright confirms what was so far hinted at, namely that he is Mulder's biological father.
- No Good Deed Goes Unpunished: A fatal example for him this time. Michael Kritschgau, despite having had his life ruined helping Mulder and Scully in the past, still came back to help Mulder with his situation in the story arc at his request. He comes to believe what Mulder does about extraterrestrials and attempts to take up the torch of his quest and bring the truth about it to light, if in a more coarse sort of way. He receives nothing but begrudging acceptance from Skinner and scathing opposition from Scully, who he helped save in the past, then for his troubles he ends up casually murdered by Krycek, his apartment set on fire, all the data he had collected stolen or burned by him, and is never even mentioned by the heroes again. The only tiny silver lining in the poor man's story is Skinner eventually avenging his murder, one season later.
- Redemption Equals Death: Fowley rediscovers her conscience and makes a turn for the better, but much like Spender before her, her reward is this.
- Shattering the Illusion: Scully (as herself, not aged as Mulder is at the time) appears in Mulder's coma at his deathbed and berates him for giving up.Scully: You're not supposed to die, Mulder. Not here.
Mulder: What do you mean?
Scully: Not in a comfortable bed with the devil outside.
- Shirtless Scene: Mulder in his dream, with Diana.
- Shout-Out: The premise was heavily influenced by The Last Temptation of Christ, with Mulder as Jesus, CSM as the Devil, and Scully as Judas.
- Shut Up, Kirk!: The Cigarette Smoking Man resorts to this while attempting to talk Mulder out of being an Inspirational Martyr.note CSM: Rise out of your bed and come with me.
Mulder: I'm dying, you idiot. If I could get up, I'd kick your ass.
CSM: Don't be so dramatic. Only part of you is dying: The part that played the hero. You've suffered enough, for your partner, for the X-Files, for the world. You're not Christ, you're not Prince Hamlet, you're not even Ralph Nader.
- Trademark Favorite Food: In Mulder's dream, the fridge is filled with bags of sunflower seeds.
- Wham Line: One dropped at the end of the cold open, with the Cigarette Smoking Man saying this to Fox:
- While Rome Burns: Mulder's "Last Temptation" dream ends with CSM in a golden spire, smoking one of his signature Morleys while overlooking a scorched, enslaved Earth.
Scully: And you are mine.