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Directed by Rob Bowman
Mulder: Well, Scully, you're a little late. I'm locked inside that train car.
Mulder explores a rail car used for secret experiments. Scully investigates the purpose and history of her alien implant.
- The Adjectival Man: Red-Haired Man and First Elder.
- Affably Evil: The Red-Haired Man, who resorts to diplomacy and talk when Mulder turns the tables on him. It might have been an act, and he was certainly presenting himself as such in an attempt to break Mulder's walls down, but the mask doesn't really drop.
- Bat Signal: Scully puts the X sign from masking tape to summon up X.
- Big Damn Heroes: Mr. X swoops in at the last minute to gun down the Red-Haired Man before he can leave an injured Mulder to his death aboard the box car with a bomb on it. He picks up the unconscious agent and carries him away from the blast radius just in time, saving his life.
- Blatant Lies: A woman and her son walk in on Mulder standing over a dead man with his throat obviously slit. Mulder blithely passes it off as "he's just got a little motion sickness".
- CIA Evil, FBI Good: The red-haired Syndicate assassin who tries to kill Mulder with a garrote claims to be an NSA agent (though it's unclear if he actually is from NSA).Mulder: The NSA? Since when did they start issuing you guys piano wire instead of guns?
- Consummate Liar: The Red-Haired Man spins a fairly convincing cover story when Mulder has him cornered, but Mulder doesn't believe a word of it.
- Deadly Doctor: The Japanese doctors.
- Disposable Vagrant: Scully is informed about horrible experiments performed on lepers, homeless and insane people. Quite interesting, actually, as they usually have no scruples about abducting anybody, not excluding their own family members.
- Evilutionary Biologist: Dr. Shiro Zama/Takeo Ishamaru.Scully: You hid him here after the war. He stayed here, and he continued his experiments.First Elder: The ruler of the world is no longer the country with the bravest soldiers, but the greatest scientists. Unfortunately, Ishimaru began to conduct his work in secret, not sharing with those who had risked much in giving him his asylum.Scully: What was he exposing these people to?First Elder: Terrible things.
- Fake Static: Mulder pretends his cell phone call with Scully has broken up before hanging up on her.
- Good Is Not Soft: Mulder, believing he and the Red-Haired Man have about thirty minutes left to live, threatens his companion with a gunshot to the stomach, explaining that he'll be dying in the slowest possible manner left to them unless Mulder gets the answers he wants.Mulder: You should know that a gunshot wound to the stomach is probably the most painful and the slowest way to die... but I'm not a very good shot, and when I miss, I tend to miss low.
- Hollywood Healing: Averted. At the end of the episode Mulder's face bears very visible and believable marks from a severe beating.
- Lab Rat: Agent Pendrell helps Scully identify her implant.
- Myth Arc
- Mysterious Informant: Mr. X appears several times.
- Omniscient Council of Vagueness: The Syndicate, represented by First Elder. The Cigarette-Smoking Man also has a brief cameo late in the episode.
- Race Against the Clock: Mulder doesn't have much time to separate the box car with a ticking bomb from the train full of people. He also needs to find out the code to open the sealed door to get out.
- Stuff Blowing Up: The boxcar, seeing as there's a bomb on it.
- Unflinching Walk: X calmly carrying Mulder away from the exploding boxcar.
- What You Are in the Dark: Mr. X has the choice between saving Mulder or the hybrid and chooses Mulder. Mulder never finds out that X saved him.