In 1897, a Russian Schooner was chartered to carry private cargo, consisting of fifty wooden crates, from Romania to England.
When the ship arrived, it was derelict.
The framing of the story begins with the discovery of the Demeter wreckage of the coast of England, in Whitby on August 6, 1897. A couple of constables find the log, and begin reading the last entry, where a message about how they tried to stop it can be seen, as well as a plea to God that whoever finds the log is safe from "It" as well.
As the book is taken as evidence to investigate, the deputy holding it gives it a read from the beginning, the narration thus taking us to the actual story.
We begin by seeing Dr. Jean-Pierre Chevalier as he is treating a young woman in one of the villages in Bulgaria. On the outside, the population of the small village are listening to their wisemen as he claims the girl to be possessed by evil spirits, and they need to send her away from the village before it brings down the "wrath of the dragon". The people are beginning to be swayed when the Doctor makes its appearance, claims to have cured her, and then dismantles all the arguments the wisemen brings about, proving that all his arguments were nothing but a way to hide what He had done to the girl.
As he prepares to leave the village, he is approached by the grateful family for having aided their daughter. He replies in a cold manner, just asking for his payment, and then prepares to leave. He takes a ride with a carriage group on the way to Varna, where he is asked about what is a Frenchman doing in the rustic area of Bulgaria, though he ignores the question. Looking instead at the cargo on the carriage, which is revealed to be many crates, some of them with the symbol of a black dragon, which the carriage driver immediately covers when he sees the doctor looking at it in curiosity.
We then turn to the city of Varna, as the Demeter arrives in port. Captain Elliot is directing his men in the correct procedures to have the ship moor for the cargo, while also speaking with his First mate, Mr. Wojchek, to get him more men for the return trip to England. We then see a small montage as Mr. Wojchek goes looking through the slums, brothels, as well as sending messages to more veteran sailors about the need for a crew for the ship. Meanwhile, the carriage with the crates are arriving at the ship, with Dr. Chevalier looking at it consideringly.
At the same time, Mr. Wojchek arrives with the prospective crew, many strong men and some who had skills needed for the ship to be maintained. Captain Elliot inspects some, and dismisses others, but overall a good number of men are set to work on loading the goods into the ship; some Turkish cotton, 10 barrels of petroleum, and some private crates for London arriving from Romania. The Carriage driver and the men with him leave as soon as they receive their payment, but not before giving a final look at the captain and his men, and praying for them once they were some distance away.
As the men are loading the final crates in, Dr. Chevalier approaches the captain and offers his services for the ship, which the captain agrees to once learning that he is a doctor, not having one with them for a while, and with many of his previous crew needing some treatment at that. The deal made, Dr. Chevalier is given the tour by Olgaren, a Russian born member of the crew, a cheerful if somewhat superstitious man who leads him through the different rooms of the ship, and where his medical station will be. During the trip, Olgaren displays his superstitious beliefs which has Dr. Chevalier scoffing at him, mocking his "primitive beliefs" as he calls them, arguing that such thoughts at the dawn of a new century should be discarded. Both sides seem to be escalating into a real argument, but a commotion outside interrupts them.
When going out they find that one of the workers suffered an accident when one of the crates being lifted was accidentally let go. When questioning the man responsible, he answers angrily by pointing to the black dragon symbol, claiming that it is an omen of bad luck, as he has heard the stories associated with it, and he will have nothing to do with it. He returns the money given to him and angrily (as well as fearfully) leaves, with some of the more superstitious workers also leaving with him. Dr. Chevalier looks at them go, shaking his head, and retreating into his work station, where he starts preparing his tools and putting everything into place.
We see a small montage of the different sailors begin preparing the ship to set sail, showing the captain working on the Log, with a narration of what went on the day, as well as showing Mr. Wojchek setting the new tasks and chores to the new hands, as well as Olgaren whose job is to feed the animals and check on the rations for the crew. We see the cook, Joseph give a prayer to God for fair weather, as he, Mr. Wojchek, and the captain begins discussing the travel ahead, whether they will need to ration the meals, and if they would need to stop at different ports to resupply.
Through the rest of the week there seems to be a sense of routine going on the ship; Olgaren feeds the animals and checks on the supplies, meals are served on time and the crew talks and interacts, with Dr. Chevalier usually staying on his own side away from the others. One of the new hands, Abrams, decides to accompany him. A young man who's never gone that far from his village, this is the first time he was selected for a job and he is curious about the world beyond it. Dr. Chevalier usually tolerates his presence, giving a comment here and there, but that's usually enough for Abrams. The rest of the crew think him a snob or "too good for them", creating a barrier, yet nonetheless going to him with the many ailments that one would get while working on a ship.
Meanwhile, Captain Elliot is seen working on the route along Mr. Wojchek, with the former eventually deciding that with their current speed and food, they could very well move directly to London without the need to stop at any port. Mr. Wojchek feels that they should at least make a quick stop in Italy, but is eventually overruled.
During the nights, one of the older crewmembers, Petrofsky, is seen to be on night watch duty, when he starts hearing odd noises, almost like someone is walking fast through the halls. He calls out to anyone there, but there is no answer. The steps move faster as well when he approaches, almost as if they're running. Petrofsky follows it on a fast chase, never seeing anyone, until he arrives at the cargo area, with no one there. He turns back to his shift above deck. However, once gone, one of the crates with the black dragon symbol seems to slowly move, as the lid lifts a bit.
By the next week the routine once more is seen, though there seems to be a certain tension between the crew, leading to more fights and arguments. One day, on the mess hall, Petrofsky recounts of the mysterious loud steps he can hear at night to the rest of the crew, mentioning the rapid footsteps and their sudden disappearance. Olgaren suspects that it might be ghosts, but Dr. Chevalier laughs at the idea, which angers the crew and ask him to explain himself. Dr. Chevalier then explains how with the night time and the rapid movements, it must have clearly been rats moving about, and chides them for not keeping a cleaner environment. This has Petrofsky go up to him and grab him, angrily arguing that he could distinguish between rats and whatever that was, while Chevalier argued that he clearly couldn't if he was stupid enough to believe in ghosts. Petrofsky gets ready to punch his face in, but is stopped by Abrams, who moves to aid the doctor. Before the situation can escalate as tempers are short, Joseph intervenes, claiming that unless they want to go on half rations that they separate and go about their business. After a moment of tension, they do so.
The next night, Petrofsky hears the noises again, and tries to once more follow them, the darkness of the ship and the inner holds keeping him on his toes. The more he delves deep the more he can feel his heart pounding as he approaches the sounds, coming closer to him now as if ready to confront him. Petrofsky prepares himself, waiting in an intersection as the steps move closer and closer, then turns to attack... and is stopped when he sees Chevalier and Abrams, both as surprised to see him as well.
When they both confront each other, Abrams tries to stop them, with Dr. Chevalier mentioning how he planned to put an end to this "superstitious nonsense", yet before another fight can break out the stepping sounds re-appear, causing the doctor to agree that's not the sound rats make. The trio then begins moving through the ship, from hall to hall, the sounds once more taking them to the cargo area once more. This time however, they all decide to move in, looking through to find just what it is that is making the sound. As they split and each move through the different crates and cargo that the ship carries, a small sound catches Chevalier's attention, softly calling to the pair and having them take position with hand signals. They approach the crate that has a symbol of a black dragon in it. Chevalier has the other two nearby prepared to attack, he slowly moves to the lid, grabs it, and quickly throws it open... revealing a couple of stowaways; a mother and her small child.
Petrofsky is angry, nearly attacking the huddling pair, but both Abrams and Chevalier stop him, telling him that this is something that the captain needs to know. Looking at their emaciated state, Dr. Chevalier takes them under his custody to treat them for diseases while Abrams continues the patrol and Petrofsky, as the senior officer at the moment, goes to speak with the captain.
As they leave, no one notices another of the crates bearing the symbol of the black dragon slowly opening, what seems to be a huge nail peeking out.