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The Blessing Way
Directed by R. W. Goodwin
Mulder is nursed back to health by Albert Hosteen's tribe. Scully uncovers evidence that someone in the FBI is working with the conspiracy, and suspects Skinner.
- Catapult Nightmare: Scully, when Mulder appears to her in her dream to reveal he's back from the dead.
- Cliffhanger: The episode concludes when Scully notices men outside Mulder's door, all while she is holding Skinner at gunpoint. This gives Skinner an opening to draw his own gun, with the two locked in a Mexican Standoff.
- The Conspiracy: This episode marks the first appearance of the Syndicate as a group.
- Drowning My Sorrows: Frohike is drinking heavily when mourning Mulder.
- Evil Brit: Downplayed with the Well-Manicured Man, who introduces himself as a member of The Conspiracy, admits outright that his motives are selfish, and is quite blunt about the murderous extremes his organisation is willing to go to. For all that, he goes out of his way to warn Scully about the danger to her life, and he claims to feel murder is sometimes not the best solution.
- It Is Not Your Time: Deep Throat and Bill Mulder appear to Fox Mulder to tell him his quest is not over yet.
- Magical Native American: Played straight in this part of the trilogy when Albert Hosteen performs a healing ritual to bring Agent Mulder back to life.
- Metal Detector Checkpoint: Scully discovers her neck implant this way.
- Mexican Standoff: Scully held Skinner at gun point, but he had a chance to also pull out his gun when she heard footsteps outside Mulder's apartment. They both have their guns fixed on one another, neither is willing to flinch.
- Mistaken Identity: Luis Cardinal and Alex Krychek mistake Melissa for Dana and shoot her outside Dana's apartment.
- Murder by Mistake: Melissa Scully gets shot when she is mistaken for her sister.
- Myth Arc
- Say My Name: Before the opening credits, Scully yells out Mulder's name near the burnt boxcar in a futile attempt to find him.
- Trademark Favorite Food: Mulder gets sunflower seeds as a present from an Indian boy because he asked for them during his fevers.
- Turn in Your Badge: Scully is done with the FBI in this episode.
- Vision Quest: While undergoing the Blessing Way ritual, Mulder sees visions of his father and Deep Throat that urge him to continue his quest for the truth.