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 Cardial 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.