Nisei Tagline: "Apology Is Policy"
A UFO in the Pacific is salvaged by the Syndicate, using the salvage ship Talapus; its salvage is surveilled by japanese intelligence. Japanese scientists, some of whom were World War II criminals, work under the american Syndicate; when their on hybridization reaches an unprecedented level of success, they attempt to leave the USA with a hybrid of theirs: they want their own country to take profit of their research. The Syndicate sends a unit of soldiers and NSA's Red-haired man to exterminate them. Scully meets many women who were abducted and had implants like her; removing the implant seems to cause terminal cancer; the implants are made in Japan. A leper colony serves as a front cover for the Japaneses' hybridization test center. Mulder is trapped in a train boxcar with a hybrid, ultimately X rescues him from the self-destruct explosion. The Syndicate sacrifices the live hybrid but salvages the Japanese medical data.
Apart from the scientists, the Japanese team is composed of embassy diplomats and people on the Japanese intelligence agencies: a team very secretive and tied to its mother country. In a project very similar to Operation Paper Clip (3X02: Paper Clip), Japanese war criminals and highly qualified scientists were given amnesty in the USA, where they were encouraged to continue their experiments on humans -- resistance to pain, extreme conditions, surgical operations and diseases. In Japan, Dr. Takeo Ishimaru "was the commander of an elite section of the Japanese medical corps known as 731" (Mulder); at least 4 other members of 731 were in the USA (those that were killed during the autopsy). Like Klemper, Ishimaru came to work for the Syndicate, extending his search for a super-soldier using alien genetic material. Ishimaru was allegedly killed in 1965, but he then took the name of Dr. Shiro Zama, perhaps beginning his top secret work for the Syndicate at the same time.
Dr. Ishimaru hid his experiments in a countryside center labelled "Hansen's Disease Research Facility". Hansen's disease is another name for leprosy. Leper colonies (or Lazar houses) were used since the middle ages to quarantine people infected with the bacteria of leprosy; an effective cure for the disease exists since the 1980s. The lepers Scully finds in the Facility are "the last". Ishimaru's center used the front cover of a "leper colony" to conduct the experiments without being bothered; perhaps it really was a rebel colony in the beginning and 'changed focus' when Ishimaru took over directorship. Of the remaining lepers, "our disfigurement forced us into the camps before there was a treatment" or so they were told: maybe they were kept this way to keep the cover intact.
Escalante (the leper Scully talks with) says "Doctor Zama would round them up in groups for treatment", groups made according to each test subject's genetic profile or according to what variation of the hybridization experiments would be conducted on them. "And then the, the ones that returned always came back worse. With terrible burns all over their bodies." Assimilation of the alien genes required exposure to radiation. "They had the Hansen's deformities", which is handy for the cover. Such test subjects were kept in the Facility.
The Syndicate has a long history of using the railway system to carry out stealth experiments (cf. the failed hybrids of 2X25: Anasazi). Transport by train is easy, impersonal and draws less attention than a full-out test facility; test subjects can be carried from one site to another and brought to the treating doctors. "Ishimaru Zama, he was using the secret railroad to conduct his tests across the country." (Scully) The quarantined and fully equiped boxcars carry identification numbers written in large digits so that they can be spotted from a satellite (we see #82594 and #82517). Their failsafe mechanism is a bomb with a countdown that is automatically triggered; the countdown is stopped when the correct code is entered on the compartment's keypad. The sensitive presence of a bomb is why the Red-haired man proceeded with strangulation instead of plain firegun murder.
In these boxcars the implants were...implanted in the abductees' necks.
Agent Pendrell, who makes his first appearance here (and already a soft spot for Scully), says it's a "neural network", "definitely state of the art", "I've never seen anything even close to this density". Of course, the best stuff comes from Japan: the implants were manufactured somewhere in Japan and sent to Ishimaru in the Perkey Facility. The functioning of the implant as described (or touched upon) is strange. By capturing the impulses coming in and out of the central nervous system (the brain) and replicating them, the microchip in the implant effectively stores all the person's thoughts, "replicating a person's mental processes". A feature of the implants that brings into mind feelings of paranoia and invasion of privacy; this feature will not be touched upon again.
The Talapus and the being on the 'alien autopsy video'
Which brings us to the story of the episodes. From the Japanese satellite photos, from what the US Coast Guard officer says and from what he saw in the warehouse in Newport News and on his $29.95 Rat Tail Productions video, Mulder concludes that a UFO was salvaged "off the bottom of the Pacific Ocean" by the ship Talapus, transported through the Panama Canal all the way up to Newport News, Virginia, where the Talapus escaped being controlled by the DEA (Drug Enforcement Administration) in the naval shipyard. The name 'Talapus' was erased from the hull and customs were told that the ship had sailed away already. The UFO was stored in a warehouse in the Newport News shipyard.
In classic XF fashion, the episodes can be interpreted in any of two ways: this was a genuine EBE or one of Ishimaru's hybrids. Lacking direct factual evidence, we can consider the plot as a whole. The main storyline involves Mulder following a traincar in which there is a hybrid created by Japanese scientists. The Japanese plan to leave the US and keep track of Syndicate activities through satellite. It makes more sense for the being examined to be a hybrid of their own making rather than an EBE from an otherwise separate storyline that is abandoned after the teaser. The salvaged UFO will resurface later in the season, the Japanese won't. I would vote for this being another hybrid.
Then the scientists were murdered by a US military platoon, the same kind of people who come after Mulder in the Virginia naval shipyard. The First Elder explains: "Ishimaru began to conduct his work in secret, not sharing with those who had risked much in giving him his asylum." Having attained a highly successful hybrid, Ishimaru and his team plan to smuggle it out of the USA. From Virginia (where the Facility is located) to Ohio (where Mulder jumped on it) to Iowa (where the train left boxcar #82517), then Vancouver (:)) and from there their home country. This triggers the extermination of the entire Japanese chapter in the US (not unlike Dr. Secare in 1X23: The Erlenmeyer Flask). The Red-haired Man, undercover agent of the NSA, was ordered by the First Elder to kill Ishimaru and his colleagues and salvage their work on hybridization. If the Syndicate could get their hands on Ishimaru's notes, the hybrid itself was expendable; which is why nobody came to rescue them as Mulder expected. The traincar #82594 and the Red-haired Man were under close surveilance from satellite, which was perhaps how X located Mulder on time. X tried to protect Mulder by not making him a target of the Red-haired Man, but Mulder boarded the train anyway. After the Red-haired Man failed ("I wasn't expected to fail"), X is sent to finish the work. He gets the briefcase with Ishimaru's notes; he doesn't have enough time to save the hybrid and saves Mulder instead.
The arrest M&S make of Sakurai nearly causes a diplomatic incident, which is why Skinner backs off from his support to the agents ("This is bigger than me, you, or the F.B.I.") and goes beyond Skinner's deal of protection with the CSM. Diplomatic channels is also why Mulder turns to his contact in the Congress, Senator Richard Matheson, for help. Matheson says he's "on the intelligence committee." More than just a generic description for his occupation, Matheson most likely refers to the US Senate Select Committee on Intelligence that overviews the activities and the budgets of the intelligence agencies (which include FBI, CIA, NSA, DEA). As in any level of the government, "some secrets do remain secret, Fox, even to me."
A shroud of lies
In her attempts to bring Mulder closer to terrestrial affairs, Scully makes a reference to a real event that might have inspired Carter & Spotnitz with the scenario: "Two weeks ago, the president made a public apology for secret radiation tests that had been conducted on innocent citizens up until 1974." Indeed, about two weeks before Nisei aired, in October 1995, was issued the final report of the Advisory Committee on Human Radiation Experiments (ACHRE), formed by President Clinton in January 1994. Among other things, the report makes a list of experiments conducted by the US government oriented on biomedical research (Manhattan Project) and space exploration (cf. Klemper and Von Braun in Paper Clip) in the period 1944-1974; it offers personal apologies to the victims and measures against such experiments in the future. The X-Files were never as topical!
In the end, Scully concludes: "What I am saying, Mulder, is that there is
no such thing as alien abduction." "You're doing their work for them. [...]
Apology has become policy." And while Mulder & Scully debate
over what they saw, CSM is happy to have the work of Ishimaru
translated to him.
Title note: 'nisei' means 'second
generation' in japanese. The term is used for second-generation
Japanese immigrants in a foreign country. Here, it is used as a
reference to the hybrid: a biological product of two initial species.
Scully: "What are you watching?"
Mulder: "Something that just came in the mail."
Scully (looks at the alien autopsy video): "That's not your usual brand of entertainment."
A reference to the infamous 'Roswell alien autopsy' video that made much fuss around that time:
Scully: "You spent money for this?"
Mulder: "Twenty-nine ninety-five, plus shipping."
Scully: "Mulder, this is even hokier than the one they aired on the Fox network. You can't even see what they're operating on!"
Mulder: "But it, it does look authentic. I mean, the setting and the procedures. I mean, it does look as if an actual autopsy is being performed, doesn't it?"
Mulder: "So you're saying that's from a German satellite?"
Byers: "No, the optics are German. The technology is probably ours, but the satellite is most likely Japanese."
Frohike: "Launched from South America."
Mulder: "Got to love that global economy, huh?"
Sen. R. Matheson: "I'm on the intelligence committee. Secrets are the only real currency we deal in."
Mulder: "What am I onto here?"
Sen. R. Matheson: "Monsters begetting monsters."
Mulder: "Scully, after all you've seen... after all you've told me you've seen. The tunnel with medical files, the, the beings moving past you, the... the implant in your neck, why do you refuse to believe?"
Scully: "Believing's the easy part, Mulder. I just need more than you, I need proof."
Mulder: "You think that believing is easy?"
Mulder (upon discovering Zama's notes in japanese): "Why did I study French in high school?"
First Elder: "The ruler of the world is no longer the country with the bravest soldiers, but the greatest scientists."
Mulder: "That's no innocent civilian. It's not a leper either. It's an alien-human hybrid, isn't it?"
Red-haired Man: "Then again, if that were true, you'd have expected someone would have been here by now to save it, wouldn't you?"
Scully: "Don't you see, Mulder? You're doing their work for them. You're chasing aliens that aren't there, helping them to create a story to cover the shameful truth... and what they can't cover, they apologize for. Apology has become policy."
Mulder: "I, I don't need an apology for the lies. I, I don't care about the fictions they create to cover their crimes. I want them accountable for what did happen. I want an apology for the truth."