The central character of Jamaica Inn is Mary Yellen a young woman of twenty-three. She has lived all her life in the tranquil village of Helford, but when her mother dies she sets off to live with her mothers sister, Patience, a pretty, lively woman who Mary has not seen for many years. Aunt Patience lives with her landlord husband at Jamaica Inn on Bodmin Moor half way between Bodmin and Launceston.
Mary leaves Helford on a bleak November day and the coach takes her a far as Bodmin where everyone else gets off. Mary tells the coach driver that she wants to go on to Jamaica Inn and he is alarmed, he tells her that coach's no longer stop there and that decent folk don't go to Jamaica Inn any more. They set off again and Mary's apprehension grows as the coach races over the moor through the wind, rain and darkness. Eventually the coach stops and the driver hurriedly deposit's Mary and her box of possessions on the roadside in front of Jamaica Inn, which is in total darkness.
Mary finds her way to the front door, which is answered by an enormous and powerful looking man carrying a lantern. This frightening figure is Joss Merlin, the landlord of Jamaica Inn. Joss drags Mary inside and then introduces her to her Aunt Patience, a poor tattered creature in a state of nervous anxiety almost unrecognisable from her former self. Mary goes to bed that night with a heavy heart, she does not want to be at Jamaica Inn, but she knows she must stay for her aunt's sake.
Mary has a natural optimism and the next day she is ready to cope with her new life. Joss has left the house early and is away for nearly a week during which time Mary settles in, finds her way around the Inn and the surrounding moor-land and gets to know her Aunt Patience better. There is a locked and barred room at the Inn that puzzles Mary but Patience begs her not to ask questions.
On the day that Joss returns to Jamaica Inn he tells Mary that she will be required to serve behind the bar that evening. As darkness falls a strange assortment of men gather in the bar. Mary finds the men a most unpleasant crowd, particularly one man, a pedlar called Harry who makes fun of a poor idiot lad who is there. Eventually Mary asks her uncle if she can go to bed. Up in her room above the porch Mary tries to sleep, but before long she hears noises outside and peering out of the window she sees farm carts and covered wagons coming into the yard and many men including those that were in the bar earlier. The contents of the wagons are being unloaded with some of the packages being put into the carts and some being taken inside and put in the locked room. Mary realises that the contents of the packages must be the results of smuggling.
Once all the wagons have been unloaded everyone leaves except Joss, Harry and a stranger, who all return to the bar. Mary creeps downstairs and overhears an argument between the three men. It is obvious that the stranger is trying to break free from the smugglers gang. Afraid of being caught herself Mary hides in the parlour. She hears Joss send Harry home, then she realises that there is someone else there, another stranger who had been hiding upstairs all evening. Joss and this second stranger close the door to the bar and Mary can hear no more, but much later when she ventures out of the parlour she finds that the outer door is open and everyone has gone, but a rope handing over a beam in the bar suggests that Joss and the stranger from upstairs have killed the man who wanted to leave the smugglers gang.
One morning, about two weeks later, Mary finds a young man in the bar helping himself to a drink. Mary shouts at him, telling him that he will be sorry if her Uncle Joss finds him there. Joss then appears and Mary discovers that the interloper is in fact Joss' younger brother, Jem Merlin, a horse thief who lives not far away across the moor.
That evening the wagons come again and take away the packages that had been hidden in the locked room. A few days later Aunt Patience becomes very panicky when Mr Bassat the local squire calls at Jamaica Inn with one of his men. He is a magistrate and he has a warrant to search the premises. The men even break into the locked room, but they find nothing. When Joss hears of Mr Bassat's visit he is alarmed and goes straight out, heading across the moor on foot. Mary tries to follow Joss, but she gets lost on the moor. A man on horseback stops to help Mary, he is very strange looking with colourless skin, white hair and pale eyes. Mary realises that he is an albino and feels more comfortable when he introduces himself as Frances Davey, the vicar of Altarnun. The vicar takes Mary home to the vicarage for tea and she tells him the whole story of what has happened at Jamaica Inn since the day she arrived. Later he drives her home to the Inn.
When Mary gets home she finds Joss in a drunken stupor and he remains the same for five days. On the fifth day Mary goes out walking on the moor and accidentally stumbles upon Jem's home. Jem hints that her uncle is involved in something worse than smuggling. Jem shows Mary a pony, formerly dapple-grey but now black, that he has stolen from Mr Bassat and intends to sell in Launceston on Christmas Eve. He invites Mary to go to Launceston with him and she agrees.
That evening Joss asks for more drink and starts to talk. He tells Mary that he is the leader of a band of wreckers who lure ships onto the rocks, then murder the people as they try to escape the sinking ships and how they rob the bodies of the people they have killed and steal the ships cargo. Over the next four days Mary stays in her room pondering over the shocking things that Joss has told her. Now she understands why her Aunt Patience is such a broken woman. Mary also thinks about Jem and wonders if he is involved in his brother's wickedness.
On Christmas Eve Mary leaves her room and sets of to meet Jem who is going to take her to Launceston in his jingle. He immediately knows that something has changed in her because she has no colour in her face and the light has gone out of her eyes. She tells Jem that she knows about the wrecking. Jem sells the pony back to Mrs Bassat who does not recognise it as the one that was stolen. Mary and Jem enjoy the day, but when Jem kisses Mary she says she wants to go home and sends him to get the jingle. Jem doesn't return and Mary sets of home by herself. The vicar of Altarnun passes her in his carriage and offers her a lift. Again she unburdens herself to him and tells him what Joss has told her about the wreckers, but he tells her not to worry as the government is planning to patrol the coast and soon wreckers will be a thing of the past.
Once home, Mary finds that Joss and his men are about to set off on a wrecking trip and they force her to go with them. Not only does Mary see for herself the horror of the ship being lured onto the rocks and the murder and robbery that goes on but she also has to fight off the advances of Harry the pedlar. She is brought back to Jamaica Inn physically and mentally broken. It is Christmas Day. Patience cares for Mary for two days and when she is well enough to come down stairs she finds that Joss has argued with Harry and locked him in the storeroom.
Jem comes to see Mary and she tells him what has happened, but she does not trust him enough to tell him what she plans to do. Joss is talking of running away so Mary grabs a chance to get to Altarnun and report what Joss and his men have done. She hurries to the vicarage but the vicar is away from home. Mary leaves him a note and goes on to Mr Bassat's house. He is also away from home but she talks to Mrs Bassat who tells Mary that Mr Bassat now has proof of Joss' guilt and that Mr Bassat and his men are going to Jamaica Inn that evening to arrest him.
Mrs Bassat sends Richards her groom back to Jamaica Inn with Mary but Mr Bassat and his men have not arrived there. Richards waits outside and Mary goes into the Inn where, to her horror, she finds Joss has been stabbed in the back. She runs back outside just as Mr Bassat and his men arrive. The men search the Inn and find that Patience has also been stabbed to death but Harry is unharmed as he was still locked in the store. Mary believes that Jem must be responsible for the murder of her aunt and uncle. Frances Davey arrives at the Inn having received Mary's note. He offers her refuge and takes her home to the vicarage.
The next day Mary is alone in the vicarage and passes the time by looking through some of the vicar's paintings and sketches. She is horrified to find a sketch of Frances Davey`s congregation portrayed as sheep with him as a wolf. Mary wonders what sort of madman she has allowed to rescue her. When Frances Davey returns home he realises that Mary has seen the picture and that she is nervous of him.
Frances tells Mary that he has had lunch with the Squire and that Jem was there too and that it was Jem who had given Mr Bassat the proof of Joss' guilt. The vicar then goes on to tell Mary that he, the vicar of Altarnun, was the leader of the wreckers and that Joss was answerable to him and that he had killed Joss and Patience. Frances knows that Jem and Mr Bassat will soon have worked this out so he must take Mary and flee immediately.
Mary and Frances set of across the moor in the direction of the coast, as Frances believes that if they can reach a ship he will be safe. However, the fog closes in and they have to seek shelter at Rough Tor, a place of high ground on the moor. Squire Bassat and his men along with Jem and the squire's bloodhounds are pursuing Frances and Mary across the moor and as the fog clears they are visible not far behind. Frances tries to climb the Tor, but Jem shoots him and he falls to the ground dead.
Mary quickly recovers from the terrifying time she has had. The Bassat's have taken her in and they offer her work, but she wants to return to Helford. One bright January morning she is walking on the moor when Jem comes along with all his possessions loaded into his cart. He stops to talk to Mary and tells her he is setting off for a new start. He kisses her and asks her to go with him and despite her plans she agrees.