Mulder orders a video tape through a mail order ad that claims to show an alien autopsy. When Scully views it with him, she questions its authenticity and Mulder points out a few things. The autopsy appears to be taking place in a converted train car and the subject, though hardly visible, has some tubes connected that have green liquid leading to or from the body. The women call several other women from MUFON to come to the house, and as Scully sits in disbelief and horror, they ask her if she had a missing period of time in her life, and whether she has an implant like theirs as they all hold up vials with similar metallic implants. Mulder shows her a picture of Japanese scientist from W.W.II consisting of the names on the senator's list. He tells her four of the men have turned up dead, all part of a group known as "731" that performed horrible medical experiments. Back on the train, Mulder enters the unlocked quarantine car and finds a locked holding cell at the back that seems to contain some sort of alien being. As he stands looking at the alien, he is surprised from behind by the Red-Haired Man who garrotes him, strangling him until the conductor suddenly bursts in. Scully is frantically trying anything to help Mulder from the outside, calling Senator Matheson and putting the masking tape X in the window to summon Mr. X. Desperately, she reviews the autopsy video for any info on the train car and notices that as Zama exits the car, she can see him punching in a code. She phones Mulder and as she watches the tape in slo-mo, she tries to make out the code as Mulder punches it in.

Nisei (part 1 of 2) Mulder orders a video tape through a mail order ad that claims to show an alien autopsy. When Scully views it with him, she questions its authenticity and Mulder points out a few things. The autopsy appears to be taking place in a converted train car and the subject, though hardly visible, has some tubes connected that have green liquid leading to or from the body. The final moments of video, show some sort of black-ops team bursting into the car in a hail of gunfire as the video feed cuts out to static. The man who sold the tape to Mulder claims to have picked it up off a satellite feed so Mulder and Scully head to Allentown, PA to check out his story. When they arrive, they find the man dead, with a pillow over his head, shot execution-style. As they examine the body, an Asian man suddenly dashes out of the house and Mulder pursues and apprehends him after nearly getting his butt kicked. The man also knocks Mulder's gun out of his hand which, if you've watched the show for any length of time, you will realize happens all the time. This time Mulder is carrying a spare gun in an ankle holster. They find out the man is a Japanese diplomat when Skinner shows up to tell them to cease and desist. Mulder is ordered back to DC, but before he leaves he shows Scully the diplomat's briefcase which he "forgot" to turn into the police. It contains satellite photos of a large ship, and a list of names from MUFON (Mutual UFO Network). Scully checks out the names while Mulder takes the photos to the Lone Gunmen to learn what he can. The diplomat is released, but as he enters a limousine, he is met by a man referred to as the Red-Haired Man who wraps a garrote around his neck and kills him. Meanwhile, Scully checks on a name from the list that was circled, a Betsy Hagopian. When she arrives at the address, two women meet her at the door and tell her they've seen her before...they know her. Neither of them is Betsy Hagopian, who they say is in the hospital suffering from terminal cancer. The women call several other women from MUFON to come to the house, and as Scully sits in disbelief and horror, they ask her if she had a missing period of time in her life, and whether she has an implant like theirs as they all hold up vials with similar metallic implants. As Scully is having quick flashes of memory that she'd rather deny, Mulder finds out from the Lone Gunmen that the ship in the picture is named the Talapus. Mulder tracks down the ship and sneaks onboard, but as he begins to search, a black- ops team shows up and he is forced to dive into the water and swim to escape. Not an easy task in Armani, loafers, and a trenchcoat. As Mulder comes ashore, he comes upon a warehouse which appears to house a UFO that he thinks has been salvaged from the ocean floor by the Talapus. When he returns to his apartment, he finds it's been ransacked. Skinner is waiting inside, saying he must have missed the party. He tells Mulder that the diplomat was found dead and asks for the briefcase. When Mulder says that Scully has the evidence, Skinner makes it clear that he's not pleased and he's removing himself from the chain of responsibility. He tells Mulder to find help covering his butt from other sources since he's on his own. Mulder turns to Senator Matheson (see Little Green Men) who tells him he should return the satellite photos but gives him a list of names representing the doctor's in the apparent traincar autopsy bay. When Mulder asks the senator what he's stumbled into, he replies, "Monsters, begetting monsters." Scully returns to DC, pretty shaken up from her encounter with the MUFON women. Two of the members, including a woman named Penny Northern, took her to see Betsy in the hospital and told her that they are all dying from what's been done to them...from an untreatable form of cancer. Mulder shows her a picture of Japanese scientist from W.W.II consisting of the names on the senator's list. He tells her four of the men have turned up dead, all part of a group known as "731" that performed horrible medical experiments. Scully seems to recognize one of the doctors in the picture but Mulder claims it's impossible since the picture is from long ago; that she might have just recognized one of them from the video. Mulder proposes that the men were attempting to create an alien/human hybrid and were killed by the government but Scully is skeptical. Mulder gets a fax from another person who wants the truth exposed. The fax shows a spy photo of a train car that Mulder says is part of "our government's secret railroad." Mulder heads to the trainyard in time to see an unmarked van transporting what appears to be a live alien onto the traincar. Meanwhile, Scully takes her metallic implant in to the FBI's SciCrime lab to have it analyzed, turning it over to Agent Pendrell. She then re-watches Mulder's autopsy video, and recognizes the Japanese doctor again, realizing that she saw him during her abduction experience. She recalls him hovering over her as she lay helpless on an examination table. At the train station, we see the Red-Haired man follow a Japanese man into the bathroom and kill him. The man was apparently meeting with a Dr. Zama for the trip, and Dr. Zama is none other than the scientist that Scully has just ID'd from the tape. Mr. X shows up at Scully's apartment to warn her that her partner is in danger; that he shouldn't board the train. She calls Mulder and reaches him as he is poised on an overpass after having chased down the train. He is preparing to leap onto the roof of the train as it passes and she urges him not to do it; that it is too dangerous and he should just let it go. But being Mulder, he can't let the opportunity pass and leaps onto the train, losing his cell phone in the process. To be continued... 731 (part 2 of 2) The episode opens with uniformed troops forcing alien-humanoid beings out of a barracks and forcing them to line up over a large dug-out area in the forest. The sign at the compound reads Hansen's Disease Research Facility. As one being, who seems to have avoided detection watches from hiding, a firing squad opens up killing all the beings as they fall into what appears to be a mass grave. Meanwhile, Mulder in a Shatneresque moment, clings tenaciously to the top of the speeding train, mourning the loss of his cell phone and probably thinking of all the paperwork he'll have to file to get a new one requisitioned. Scully, in her apartment with X, tries to get more information from him, even holding a gun on him. He disarms her, then tells her if she wants to find out about the train and the people that killed her sister, she should be looking into the implant from her neck. He says it holds many answers, "maybe everything you need to know." She returns to Agent Pendrell, who has discovered that the chip is basically a tiny microprocessor that works like the brain's memory...so anyone accessing the information could know your every thought. He says the chip has a Japanese manufacturer whose only traceable shipment was to a disease research facility in West Virginia. Meanwhile, Mulder boards the train and finds Dr. Zama's compartment. Dr. Zama isn't there but Mulder finds a briefcase and several journals with entries in Japanese. The compartment is empty because Zama is currently being garroted by the Red-Haired Man in the public restroom. Mulder, searching for the doctor, finds him dead and asking the help of the conductor in concealing the body from the other passengers, learns that the doctor may have been on board to supervise whatever is being transported in the rear quarantine car. While Mulder is heading back to find the quarantine car, Scully has driven to the Hansen's Disease Research Facility. She finds the place deserted except for some leper patients who were hidden beneath the floor boards of one of the barracks. One of the men tells her that the medical staff left then the death squads came to eliminate all those remaining. He leads her to the mass grave and she sees the truth of his story. He tells her the others were subjected to experiments and would often come back horribly burned but not dead. Just then a helicopter circles overhead with a bright light shining down to pin the two. The man runs into the woods and Scully is detained as she hears gunfire in the distance. She is lead to the barracks where the Italian Elder (part of the consortium) tells her that the remaining people, part of an inhuman project, have been terminated but that he has something to show her which might answer some of her questions. He leads her to a train car which has been converted to a medical facility. It is identical to the one from Mulder's video, and it conjures a memory for Scully from her abduction. She is convinced that she was held and experimented on in a similar train car during her missing time. Back on the train, Mulder enters the unlocked quarantine car and finds a locked holding cell at the back that seems to contain some sort of alien being. As he stands looking at the alien, he is surprised from behind by the Red-Haired Man who garrotes him, strangling him until the conductor suddenly bursts in. During the interruption, Mulder frees himself and pulls a gun on the man who identifies himself as an NSA agent. When he appears to make a suspicious move, the conductor rushes from the quarantine car, slamming the door behind him effectively locking in Mulder and the NSA agent. He tells Mulder that there is a bomb on the train and that they are now locked in since a code is needed to exit...a code that he doesn't have. Mulder checks the man's ID and it does show him to be an NSA agent. As they tensely stand with Mulder training his gun on the man, Mulder decides the bomb must be on their car just as a beeper sounds. Both of them flinch until they realize it is the NSA agent's cell phone. Surprisingly, the call is for Mulder. It is the Elder who hands the phone over to Scully. She tells him what she's seen and discovered and informs him that she believes the being on the train is not an alien, but a human subject that has undergone experimentation. She tells Mulder she thinks alien abductions are just a smokescreen and cites her own disappearance as proof. Mulder asks what about the Talapus and the UFO he saw? She says there have been recent reports about continued, unsanctioned nuclear testing and that his "UFO" was probably just a salvaged ship. She tells him that the Elder informed her that the subject on the train is infected with a disease that will kill thousands if the bomb detonates. In order to put the least amount of people at risk, Mulder suggests that the train conductor unhook the quarantine car as far from a populated area as possible. He and the NSA agent locate the bomb and find themselves with less than two hours to find a way to de- activate it. Mulder believes that the alien/human hybrid is so important, someone will come to retrieve it saving all of them. But as the minutes tick by, there is no sign of rescue. He asks the NSA agent what the being is and after some threats, he suggests it may be a hybrid immune to the effects of biological warfare, making it a powerful weapon. Mulder speculates that our government didn't want to share the science, so when Zama tried to smuggle the alien out, they sent forces to destroy the research and kill the doctors involved. The NSA agent seems to agree then says, "But if all that were true, you'd think they'd send someone to retrieve it." Meanwhile, Scully is frantically trying anything to help Mulder from the outside, calling Senator Matheson and putting the masking tape X in the window to summon Mr. X. Desperately, she reviews the autopsy video for any info on the train car and notices that as Zama exits the car, she can see him punching in a code. She phones Mulder and as she watches the tape in slo-mo, she tries to make out the code as Mulder punches it in. Unsure about the final digit, she makes her best guess and as Mulder enters it and gets a green light, he is suddenly cold-cocked from behind by the NSA agent. He lingers to beat the sh*t out of Mulder with a few well-places punches, but as he exits the car he is shot in the stomach and falls to the ground. Mr. X steps over the body, checks on Mulder, then walks to the back of the quarantine car and looks into the holding cell where the hybrid is locked. With less than a minute, there isn't time to accomplish everything and X carries Mulder's bloody body away from the train car as it explodes on the tracks. A week later, Mulder has learned little else about the train car or its contents and the briefcase and journals that were retrieved from Dr. Zama's quarters are not the ones that Mulder originally saw. They have been replaced. "They're getting away with it, Scully," he says. "They've gotten away with it, Mulder," Scully responds. She comments that what they can't cover up they apologize for, "Apology is policy." Mulder says what he wants is an apology for the truth. The dual investigation that the agents undertook, has left them with their belief systems more firmly intact than ever. Believer and skeptic. Mulder seeing alien involvement, while Scully sees government elements at work. The episode draws to a close in a poorly lit room where a Japanese man is transcribing from Dr. Zama's journals while CSM looks on.