“731” is episode ten of season three of The X-Files.
This episode opens in Perkey, West Virginian, and military trucks ram the locked gates of a compound that has an old and fading sign reading ‘Hansen’s Disease Research Facility.’ Armed soldiers leave the trucks and enter a building, herding the residents, who are never seen clearly, out. Someone is watching this from a trapdoor in the floor. Something looks off about the residents. They are herded outside and the watcher under the floor gets out and watches the others being herded onto trucks. Something is off about him as well, but it looks like it’s off in a different way. Those herded onto the trucks seem to have too many joints in their fingers.
The watcher heads through the trees and sees the others, now no longer in the trucks. The shape of their heads is wrong and they are all bald. The watcher himself has hair and some sort of skin condition. The others are told to turn around; some appear to have the eyes of Greys. They are gunned down by the soldiers and drop into a trench.
The opening phrase in this episode is ‘Apology is Policy.’
At the end of the previous episode, “Nisei”, Scully called Mulder as he was about to jump onto a train containing one of the unusual cars, as Mr. X had told her she had to stop him from getting onto it. Mulder jumped anyway, and dropped his phone whilst doing so. This bit is shown again, then Scully asks Mr. X what’s on the train. He tells her it doesn’t matter. She says that something was put on the train in West Virginia, something living, and the Japanese are involved somehow. He’s leaving and, when Scully points her gun at him, takes it out of her hands.
Mr. X explains that there are limits to his knowledge. Is she going to kill him, like the men killed her sister? If she wants to know what’s on the train, who killed her sister, find out about the implant put into her neck. It can tell her more than he could, maybe everything she needs to know. He hands Scully her gun back and leaves.
Mulder manages to get inside the train, but finds a locked door with a keypad leading into the carriage. He finds the conductor and tells him he’s an FBI agent and needs access to the carriage. Not even the conductor has access. They have these cars a number of times and never know what they are carrying. The conductor believes a Japanese doctor, Shiro Zama, who is also on the train has access. Mulder asks to be taken to Zama’s compartment, which is empty of the doctor, and finds a briefcase, which he wants the conductor to keep safe. He also gives the conductor his backup gun, unloaded, to use to keep Zama controlled if he returns before Mulder finds him.
Scully is at the FBI, being briefed by Agent Pendrell about the chip. He explains that it is collecting information and replicating mental processes. It would be able of knowing every thougyh of the implanter. The chip was effectively destroyed during the test, but Pendrell found the name of the manufacturer, a Japanese company that doesn’t seem to really exist. He did find one shipment for the company, in the name of Dr Shiro Zama to Perkey, West Virginia.
Zama is on the train and the man who killed Kazuo Sakurai follows him to a toilet, attacking just before Mulder passes. Scully pulls up to the compound in Perkey, and sees several people run. She enters the building and finds the trapdoor in the floor. There are several people underneath, all suffering from something, who asks her not to kill them. On the train, Mulder notices the toilet and finds Zama inside, garrotted.
The people in Perkey say they have lived there most of their lives. They suffer from Hansen’s disease. This is a leper colony. Or was; it’s closed now. Dr Zama is not there any longer, nor are any others of the medical staff. They left before the death squads arrived. They thought Scully had come to kill them like the others. Hundreds have been killed; they are the last. Their disfigurement forced them into the camps before leprosy could be treated.
The others, though, were not lepers. They were kept separate and had deformities. Sometimes, Zama would take them away for treatment and they would come back worse. A leper leads Scully to a mass grave, where the people at the beginning were killed. There are many pits like this. Ab helicopter arrives at this point and the leper runs. Scully is surrounded by armed soldiers and she hears shots.
On the train, Mulder tells the conductor to seal the bathroom, and not to stop the train until he finds the killer, then heads to the now-unlocked carriage and enters. There’s someone in a room at the end. Unfortunately for Mulder, the carriage is wired with explosives. Scully is taken to meet one of the Smoking Man’s confederates, who seems to be oddly helpful.