Mulder is trapped on a train carriage with a ticking bomb and a killer who claims to be an NSA agent. (Part 2 of 2)
At the Hansen's Disease Research Facility soldiers arrive and round up a group of deformed patients. As one of the patients hides in the woods and watches, the patients are all gunned down by the troops and pushed into a mass grave.
Scully loses contact with Mulder, who loses his cell phone as he jumps aboard a moving train. Scully questions X on how to help him; he tells her to look into the chip that was removed in her neck, which will help her learn more about the train and who killed her sister. Mulder enters the train and talks to the Conductor, trying to get access to Dr. Shiro Zama. Inside Zama's compartment they find journals hand written in Japanese. Mulder leaves the Conductor with his (empty) backup pistol in case Zama returns.
Scully sees Agent Pendrell ,who tells her that the chip replicates the brain's memory function and can enable someone to know a person's every thought. By poking and prodding it, Pendrell has effectively destroyed the chip. They find the manufacturer of the chip to be a Dr. Shiro Zama from a disease research facility in West Virginia.
As Mulder searches the train for Dr. Zama, the Red-Haired Man corners Zama in a bathroom and strangles him. Mulder soon finds the body when he doubles back through the train.
Scully heads to the Hansen's Disease Research Facility, where she finds a group of diseased patients hiding underneath the floor. One of the patients, Escalante, tells her that lepers and other deformed people came to the facility for treatment, but instead were experimented upon by Dr. Zama. He tells her that the medical staff left and that soldiers arrived, killing all except those who hid. Escalante shows her one of several large pits filled with corpses. Immediately afterwards a helicopter and troops arrive, shooting Escalante and capturing Scully. Mulder heads to the quarantined train car, and looks into the locked section to find an alien-like person inside. The Red Haired Man attacks Mulder, causing the Conductor to lock the two of them in the car. The Red Haired Man claims to be an agent of the National Security Agency and informs Mulder that there is a bomb on the train, which activated the moment he opened the locked car with Zama's security code.
Scully meets the First Elder, who tells her that the people at the HDR facility were part of an inhuman experiment by Zama. The First Elder permits Scully to contact Mulder by calling the Red Haired Man's cell phone. Scully tells Mulder that alien abductions, including her own, had nothing to do with aliens but rather were experiments conducted by people like Zama, with the alien abduction theory simply being a smoke screen. Scully believes that the quarantined patient in the car has hemorrhagic fever and thousands will die of it if the car explodes. Mulder finds the bomb inside a ceiling vent, with approximately 100 minutes remaining.
Mulder tells the Conductor to disconnect the car from the rest of the train in an unpopulated area. The Red Haired Man tells Mulder that the quarantined patient is a weapon, having an immunity to biological warfare. Zama tried to sneak it out of the country, but the government would rather see it destroyed than let the Japanese steal the technology. Mulder believes that the patient is an alien human hybrid. Scully tries to contact Senator Matheson and X but has no luck. By watching Mulder's alien autopsy video she figures out the car's exit code, which she repeats back to Mulder. As Mulder opens the door out of the train he is jumped and beaten unconscious by the Red Haired Man. As the Red Haired Man is about to leave, he is shot to death by X, who enters the car and, after glancing at the human-alien hybrid, carries Mulder to safety just as the car explodes.
A week later, Mulder finds himself unable to get any information on the car. Scully returns the journal he found in Dr. Zama's briefcase, but Mulder can tell that it is a rewritten substitute. Scully tells him that theirs is a fight they can only hope to lose, and the whole alien conspiracy is the government's way of trying to make amends for past atrocities, citing "apology is policy." Meanwhile, the real journal is translated in a shadowy room as the Cigarette Smoking Man watches.
- At 44:10, the Japanese man reads the Japanese book from left to right. But the Japanese alphabet is written from top to bottom.
- Two cameras were destroyed while filming this episode.
- Unit 731 was a real-life Japanese army unit in World War II that conducted sadistic medical experiments on prisoners of war and Chinese civilians. Like some of their Nazi counterparts, these scientists were set free after the war. Rumors exist that during the Korean war field testing of biological weapons were used with the assistance of a number of these scientists.
- The tagline to this episode is "Apology Is Policy".
- If you look at the Japanese diary that Mulder flips through early in the episode (In Dr. Zama's train compartment), you will notice that all the pages contain exactly the same text.
- If you watch closely you can see that Mulder runs the keycard through the door scanner the wrong way, scanning nothing but plastic.
- The name of the doctor, Takeo Ishimaru, and his alias, Shiro Zama, is an amalgamation of the name of the real head of Unit 731, Dr. Shiro Ishi.
- Scully mentions a phone call pinpointing Mulder's location that came from Blue Earth, Iowa. In reality, there is no Blue Earth in Iowa, although there is one in Minnesota.
Cast and Characters
- Michael Puttonen (Conductor) previously played Motel Manager in The X-Files episode "Deep Throat" and Dr. Pilsson in "Sleepless".
- Colin Cunningham (Escalante) previously played Lieutenant Terry Wilmer in The X-Files episode "End Game".
- Stephen McHattie the Red-Haired Man
- William B. Davis as Cigarette Smoking Man
- Michael Puttonen as Conductor
- Robert Ito as Dr. Takeo Ishimaru/Shiro Zama
- Steven Williams as X