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.
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 was mistaken for her sister, agent Scully.