The novel's protagonist and narrator is a man of advancing years who, while vacationing at a country cottage, discovers a metal box which contains five jars. Labels on the jars indicate that the ointment in them should be applied to the eyes, ears, tongue, forehead and chest. After applying the ointment, the narrator gradually gains the ability to communicate with animals and the ability to see, hear and talk to some fairy-like little people. He quickly befriends two of those little people, boys named Slim and Wag. The narrator also finds out that there are some malevolent witches and wizards who want to take the five jars away from him.
Although The Five Jars is now in the public domain in the United Kingdom and many other countries, it remains copyrighted in the United States until 2021.
The Five Jars takes the form of a letter written by the narrator, who later says that he wants to be referred to as M. or N., to someone named Jane. The narrator states that he had previously told Jane that he knew something because he had heard it from owls. Jane was puzzled by that remark. In his letter, the narrator explains how he came to be able to understand owls.
While vacationing at a country cottage, the narrator falls asleep beside a stream. He has a dream about a plant that he has never seen before. When the narrator wakes up, he hears the stream make a sound that sounds at first like "Trickle up" and later like "Track up" and "All right." The narrator follows the stream upstream to its source. The water then tells him to quickly gather and pick up something. He finds the plant that he saw in his dream. He picks the plant. It curls up into a small ball. The water tells the narrator to swallow the plant. The narrator then gains the ability to see things under the ground, when he chooses to do so.
Using his ability to see things under the ground, the narrator sees something that looks like a large flat stone. Using a penknife and his hands, the narrator digs up the object. He discovers that it is really a metal box but finds that he cannot open its lid.
The narrator leaves the box on a windowsill of the cottage where he is staying. When the moonlight touches one side of the box, the narrator hears a snap. He notices that one side of the box has opened. He moves the box so that its other three sides are also exposed to the moonlight. He is then able to open the box. He finds that it contains five glass jars. Writing on the tops of the jars in Latin say that the ointment inside them should be applied to the eyes, ears, tongue, forehead and chest. It is past midnight by that time. The narrator decides to wait until the following morning before applying any of the ointment.
The narrator wakes up very early the following morning. When he sees how early it is, the narrator decides to go back to sleep. He has a dream in which an old man in ancient Roman dress lets him know through actions and gestures that he must only apply the ointment at night. He must let the moonlight open the box each time, wash his hands before touching the jars and use a small silver spoon inside the jar to apply the ointment. The narrator follows the advice from his dream. He waits until night falls before putting some ointment from the appropriate jar onto his ears. He immediately gains the ability to understand animals' speech. He also finds that he can hear other, more human-sounding voices. He cannot, however, see who is speaking.
The following night, the narrator applies some ointment from the right jar to his eyes. He can then see who those other voices he could hear belong to. They belong to people about six inches high who live in a village of small houses on the cottage's lawn. Some of the little people, four boys, climb up to the windowsill and have a good look at the narrator. They laugh at his big nose and wonder if his kind have the ability to speak. The narrator speaks to them but they apparently just see him open and close his mouth without hearing any words. At ten o'clock, a bell sounds. The boys leave and go back to their village. The village then slowly sinks beneath the ground.
After the village disappears, a mist descends on the lawn. The narrator sees seven pillars of mist that have dull red eyes and are whispering to each other. They advance towards the house. The narrator then hears a noise when an old horseshoe falls off the mantelpiece. Remembering a superstition that he had heard about the protective powers of iron, the narrator puts the horseshoe on the windowsill. The pillars of mist stop moving towards the cottage. They fall silent and disappear. The narrator is certain that the pillars of mist were beings that wished him harm. After he goes to bed, the narrator realizes that beings wanted the box that contains the five jars. He gets up to check on the box. He finds that it is still in the closet in which he put it but the closet door is now unlocked. The narrator is certain that he locked the closet door and that nobody else has been in the room. He puts the box in his suitcase. He locks the suitcase and puts its key on the chain of his pocket watch. He sleeps with the pocket watch under his pillow.
The following morning, the narrator goes out. He sees some more of the little people who do not realize that he can see them. He also sees a red-faced old woman who is clearly not an ordinary person because she is amusing herself by swinging on a clothesline. When the old woman realizes that the narrator can see her, she becomes embarrassed and runs away. Shortly afterwards, the narrator sees the old woman again and speaks to her. The old woman realizes that, because the narrator is able to see her, he has the five jars. She tells him that he is the first person to have owned the jars since they belonged to a Roman named Vitalis. He lived in a villa by the stream one thousand four hundred years ago, at a time when the old woman was a little girl. The old woman warns the narrator that some other beings will try to take the box from him. When the narrator asks her who those beings are, she says she is not allowed to say. She gives him some four-leaved clovers and tells him to put them on the box.
When the narrator returns to the cottage, he sees an extremely old and ugly woman going towards it. Three horseshoes nailed above the cottage door prevent her from going inside it. She asks the narrator what time it is. He senses that she wants to see the key on his watch-chain. Fortunately, he does not have to take out his pocket watch because a clock inside the cottage chimes one almost immediately. The narrator tells the ugly old woman that it is one o'clock. She then has no choice but to leave. When the narrator gets inside, the maid tells him that the cat has been protecting his suitcase by sitting on it all day.
That evening, the narrator puts some ointment from the appropriate jar on his tongue. He then gains the ability to talk to animals and the little people. He invites the boy little people to come into the cottage. He quickly befriends two of them, named Wag and Slim. He teaches the boys something about the human world and they teach him something about theirs and the magical abilities that they have. He finds out that the boys are taught by owls. The narrator says to the boys that he thought that their kind had the ability to fly. They tell him that they are able to fly but have been temporarily banned from doing so due to some misbehavior. The ban is due to expire in two nights' time.
The following day, there are four attempts by the malevolent beings to take the five jars away from the narrator. A noise is made which sounds as if the maid has had an accident while dusting a shelf in the neighboring room. The narrator is about to go and help her. He then finds it strange that his landlady has not immediately gone to help her. He also notices that his suitcase has moved a little and that there are scratches on the lid. Later that morning, the narrator looks out of the window and sees an old man being attacked by dogs who is crying out for help. When the narrator looks through some binoculars, however, he does not see the old man but a cloud of vapor instead. In the afternoon, an ugly old peddler comes to the cottage and asks to see the gentleman who is staying there. The maid shoos him away. The narrator smells an unusual smell and finds himself becoming drowsy. The cat wakes him up by scratching his hand. He is just able to stop his suitcase from going out of the window in time. To protect the suitcase, the narrator puts some objects made out of iron, an element that witches and evil spirits are traditionally said to abhor, on top of it.
In the early evening, the narrator goes out for a stroll. He overhears the conversation of a family of owls that are just waking up. He understands from the owls' conversation that a final attempt will be made to take the five jars on the night of the following day. After that night, the malevolent beings will not be able to try to take the five jars again.
The narrator puts some ointment from the appropriate jar on his forehead but does not notice any immediate change. Slim, Wag and the other boys arrive. Wag gives the narrator a message from his father about the attempt that will be made to take the five jars the following night. He is told that if there is a "bat-ball", he should use an insecticide spray pump to squirt water at it. The boys notice a book and ask the narrator what it is. The narrator demonstrates by reading to them from Charles Dickens' Pickwick Papers. After he has finished reading, Slim comments that a book is, "Something like a glass." The boys also comment that by, "looking... like we do at school", they are able to see an unpleasant old man and old woman.
After the little people leave, the narrator sees a young man arrive at the cottage. The young man is, "'dressed in the fashion of eighty or ninety years ago" as we read in the ghost stories." The narrator then sees an old man and an old woman inside the cottage. The narrator realizes that they are the young man's parents. Although they look respectable, the narrator senses that they are thoroughly unpleasant. Although he cannot hear their conversation, the narrator understands that the parents do not approve of the woman that the young man wants to marry. The narrator realizes that he has gained the ability to see past events when he chooses to do so. The following day, he finds out from his landlady that the cottage was once home to an old couple who disinherited their son because they did not approve of his marriage. Their son and his wife emigrated to America and never returned. The narrator also later finds out that the little people are taught at school how to see past events in order to learn history.
The narrator goes to the tool shed to get the insecticide spray pump. He sees an old man dressed as a handyman come out of the shed. The old man has the spray pump in his hands and says that the narrator's landlady said he could borrow it. The narrator says, "what a lot of horseshoes you people leave about." He holds a horseshoe out to the old man. The old man reaches out and touches the horseshoe as if some force compels him to do so. He cries out in pain, drops the spray pump and runs off. The narrator explains that after witches and wizards touch horseshoes they have to go over all the ground that the horseshoes have been over since they were last touched by a blacksmith.
The narrator goes into the living room. There is a knock on the door. The maid appears to come in to take out the laundry. She keeps her back to the narrator. When she comes across a horseshoe, she screams in agony and flees from the room. The narrator notices that her feet are greenish and webbed. No further attempts are made to take the five jars until the evening.
When evening comes, the narrator places the box by the window so that the moonlight can open it. There is, however, something in front of the moon that is preventing its light from touching the box. The narrator realizes that it is a cloud of bats that are gradually forming themselves into a solid ball. The bat-ball approaches the window. The narrator squirts water at it with the pump spray. Wag, Slim and the other boys arrive. Although they have no wings, they are flying. They encourage the narrator to keep fighting the bats. As the bats' wings become soaked with water, they become unable to fly and fall to the ground. After a few of the bats have fallen away, one of the little people tells the narrator to throw a horseshoe at the bat in the center of the ball. That causes some of the bats to catch fire and the rest of them to fly away. The bat-ball having failed to take them, the narrator knows that the five jars are now safe forever.
The narrator puts some of the ointment from the appropriate jar on his chest. Wag tells him that his father would like to invite him to his house. The narrator thanks him but says that he will not be able to go there because of his size. Wag says that he will because after having applied the ointment from the fifth jar to his chest he has gained the ability to go anywhere. As the narrator goes towards Wag's house, he shrinks in size so that he is able to go inside it. He is introduced to Wag's family. Wag shows the narrator a "glass", the equivalent of a book to the little people. It looks like a mirror in a frame with two knobs on it. When Wag turns one of the knobs, the narrator begins to see a moving picture story. When Wag turns another knob, there is also sound to go with the story. The narrator likens the experience to watching a film in a cinema. He sees a story about a knight fighting some dragons. Before the story is finished, however, the bell sounds that indicates that the village is about to sink beneath the ground. The narrator has to leave.
At the conclusion of his letter to Jane, the narrator says, "I have not, of course, told you nearly all there is to tell." He adds that he may tell Jane more of his story later if she wishes.