“Apocrypha” is episode sixteen of season three of The X-Files.
This episode opens in a Navy Hospital in Pearl Harbor in 1958. A man is being recorded; he is telling three others that the Navy wanted to hear the truth. The man is in bed and he says he is the last who know what killed the men aboard the submarine. Those who sent them knew it was a suicide mission and he’ll burn in hell before he tells the murderers who sent them there.
One of the men says that they need to hear his story, to make sure justice is served. The dying man says that Johansen did what he had to do. In the previous episode, “Piper Maru”, Commander Johansen had told Scully what happened onboard the submarine. When he shut the captain in the room, black oil filmed over the captain’s eyes. The dying man says that finally they saw the enemy that was killing them. The enemy was struck from behind after being shut in, and oil leaked out of him, disappearing down a grate in the floor.
The dying man says that was the enemy; an entity. They were told they were trying to recover an A-bomb, which is how they got the radiation burns. He doesn’t believe that; they were sent to guard it. They were exposed to the radiation before it went back into the sea. The thing is still down there, though the Navy may deny it. He wants the three to make sure the truth gets out. He can trust one of the men to do it can’t he? Mr Mulder. That could be seen coming. One of the two other men says nothing. The third man lights a cigarette and says the dying man can trust them all. Guess who that is.
In the previous episode Skinner was shot and Scully is arriving at the hospital looking for him. She speaks to agents Fuller and Caleca, who say they got a call from DC police. The handgun used was found with no prints and was also unregistered. Skinner is wheeled out; he came through surgery okay. He tells Scully he recognised the man who shot him. Which means this wasn’t random; Skinner didn’t get shot whilst he tried to prevent a robbery. Meanwhile, Krycek and Mulder are landing at Dulles. Mulder doesn’t know the black oil has transferred itself to Krycek. In the hospital, Scully is looking at Skinner’s chart and tells the other two she wants a guard on Skinner, even if they have to do it themselves, as it wasn’t random.
Mulder and Krycek are on the road at night when a car pulls away as they pass, and follows with its lights out. It comes up behind them and rams them off the road. Two people get out. One takes Krycek from the car, asking where the tape is. He leads him away and, as the other goes to Mulder, there is a scram and a bright light. The second goes to see what happened and the same thing happens. Mulder passes out. Later, the Smoking Man is being shown the two men. They are dying the same way as the French sailors. He wants the bodies destroyed. The Navy doctor says they aren’t dead. Well, isn’t that the prognosis?
Mulder comes around in a hospital bed to find Scully there. He explains what happened, and that Krycek was there; he was selling the information from the digital tape. Mulder thought the two men planned to kill them. Scully explains about Skinner and has two transparencies. They are identical. One is from the man who shot Skinner; the other the one who shot Melissa. Definitely not random.
The group that the Smoking Man works for is meeting. They seem to be a bit disturbed with how he has been responding to the situation and have asked him to come and explain himself.
Scully tells Skinner about the man who shot him, and about how he shot Melissa. Skinner explains that he was warned off pursuing Melissa’s investigation. No, he isn’t advancing a conspiracy theory that Melissa’s investigation was topped not due to a lack of evidence but because some don’t want it solved. And as to seeing his shooter before; he was with Krycek when Skinner was attacked in the stairwell and the digital tape stolen.
Mulder has had the diving suit flown in. He tells Scully about the black oil found on the suit, Gauthier and Gauthier’s wife – who turned up in Hong Kong. The oil is diesel oil, used in P51 Mustangs and submarines, but has been altered by exposure to radiation. Mulder thinks it is the medium used by an alien creature which jumps from body to body and spent 50 years underwater waiting for a new host. And that he thinks it’s in Krycek now.
Mulder uses the Lone Gunmen with Krycek’s key to recover the digital tape from where Krycek had stored it. It’s missing, though. Krycek has taken it to the Smoking Man. Who was expecting him and isn’t bothered about the oil in Krycek’s eyes. The Smoking Man seems to be keeping some things secret from his own group, and Mulder encounters one of them again. He knows some things they don’t.
There’s one funny bit where the Lone Gunmen talk about this highly advanced equipment used to lift the imprints of writing, as Mulder is managing to get it himself. With a pencil.