"Oh Lord, we pray Thee, not that wrecks should happen, but that if they do happen, Thou wilt guide them to the coast of Cornwall for the benefit of the poor inhabitants".
So ran a prayer in the early XIX Century, before there were formal lighthouses, in Cornwall, a lawless corner of England . . .
A ship is off the coast, making its way towards the shore on a stormy night. A man leaves Jamaica Inn on horseback and goes to the bluffs to conceal the warning light and cause the ship to run aground. A band of men wait on the shore for the inevitable shipwreck. As the frigate grinds itself to death on the rocks, the men kill all the surviving sailors and loot the cargo.
It is daytime, and a stagecoach is on a road along the coast. The driver says to his companion that "Queer things" go on at Jamaica Inn. Inside the stage coach, a young Irish woman Mary Yellen (Maureen OHara) comments that she intends to stop at Jamaica Inn, whereupon those who hear her seem dumbfounded and horrified.
Mary first tells, then yells at the coachman to drop her off there, but he rudely speeds past the place and stops near the mansion of Sir Humphrey, the local squire (Charles Laughton). She gets out to complain, but the coachman throws her trunk to the ground, tells her to ask Sir Humphrey for help, as he has a soft spot for young women, and drives off.
Sir Humphrey is having dinner with upper class friends inside, grandly spouting off upper class platitudes. The butler tells him that a young woman has come and asked for him, so he leaves the dinner and goes to meet her. She reveals to him that she needs to go to Jamaica Inn to find her aunt Patience, wife of the innkeeper, and intends to move in with them, as her mother has recently died . Sir Humphrey is much struck by her beauty, offers his support and help anytime she needs anything, and orders a servant to prepare two horses so they can ride to the inn and carry her trunk.
At first Mary mistakes the rude man who answers the door to be an underling, when it is actually her uncle Joss Merlyn (Leslie Banks). Reunited with her aunt Patience (Marie Ney), a kindly woman bullied by a husband she loves, she is assigned upstairs room and told to get settled. She finds her aunt is totally under the thumb of the vicious Joss, and also senses that something evil is afoot at the inn.
In the rooms below, dirty men are drinking and singing loudly as the uncle joins them in the merriment. The uncle is the leader of this band of thieves. They are complaining that the recent wrecks have yielded very little money, and suspect a skimmer in their midst. Suspicion falls on the newest member of the gang, Jem Trehearne (Robert Newton). He is searched and found to have a large amount of money on him, which in their eyes prove his guilt, so they knock him unconscious and set about to hang him
While this is going on, the squire has come back to Jamaica Inn to talk to Joss, as it is the squire who receives the contraband and fences it, keeping an enormous cut for himself. The squire and Joss argue about various things but Joss is no match for the squire in intelligence or education or connections, so he grumblingly caves in to everything the squire wants.
Meantime, Mary from her upstairs room hears the lynching plan and spots the unconscious Jem through a hole in the floor. The drunk men fit a rope over a beam and prepare to hang him. They leave the room to look for a suitable plaform, and Mary finds the opportunity to cut the rope and drag Jem out. He recovers consciousness in the nick of time, and flees outside. Meantime the lynching party returns, finds the cut rope, figure out that Mary has helped him, and comes after her. She manages to get to the roof outside, without being seen, and there finds Jem, also hiding. Joining up, they manage to elude all parties searching for them, and get away.
The squire, meantime, has been entertaining guests at his house, guests from whom he learns about the next ship that is to approach the coast and might be lured to be wrecked and looted. Joss shows up and must give the unpleasant news to the squire.
Jem and Mary have made their escape in a row boat to a cave along the shoreline below the inn, where they slept. Mary wakes first, decides she no longer wants to be with an outlaw, and prepares to row away in the rowboat. Jem wakes, attempts to stop Mary, and, distracted by their arguing, the row boat slips off the shore and floats away leaving both of them stranded in the cave. Unfortunately, their small row boat is spotted by the thieves, who know about the cave and figure out where they are. That cave can be reached from the top of the bluff by a small hole, so the thieves prepare to go down the small hole to reach the pair, and send for a larger boat to come. Slipping into the water, the pair hides behind a rock near the surf zone some distance from the cave as the thieves' boat passes by. They eventually make their way to shore, where Mary suggests they flee to the squire's home for assistance.
At the squire's house, Mary is led away to be given dry clothes. When she has gone, Jem reveals to Sir Humphrey that he is actually a lawman, an officer in the Royal Navy, who has been dispatched to uncover the thieves and bring them to justice. He suspects that there is another man behind the capers, someone who is sending the thieves information about what ships to lure and at what time, but he hasn't learned who that is. The squire furnishes Jem with officer's clothes, and offers to help directly, as he is the ranking magistrate in the area. They both grab their pistols and charge off to the Jamaica Inn to arrest Mary's aunt, uncle, and the gang for piracy, after sending a message to a garrison of the squire's knowledge, led by his supposed friend a Captain Boyle, to come help capture the gang. Mary overhears the arrest plan, steals the carriage to go warn her aunt and uncle, so that they may escape the hangman's noose.
Jem and the squire arrive at Jamaica Inn before Patience and Joss get away, and they are arrested and held at gunpoint. Mary is upset at having been deceived by Jem, in that he has let her think he was an outlaw, and for insisting that Patience has been in the gang all along. The Squire manages to send Jem away sufficiently long that he is able to communicate to Joss the timing and location of the next ship that is expected, and insists to Joss that the ship must be looted as all the others, despite the inconvenient fact that Jem knows about the gang. He desperately needs more money.
The gang arrives and with the Squires connivance, manages to free Joss and tie up the squire and Jem onto chairs. The gang is very keen to go trigger the wreck and get their next load of loot. They leave Patience holding a gun on the two prisoners, and take Mary with them as hostage. After the gang leaves, the squire calmly takes off his ropes, as his ropes had not really tied him down, and leaves, threatening Patience with harm to Joss if she disobeys. Jem works on Patience's conscience, telling her that she is helping to murder a large group of husbands, the officers and sailors on the ship, if she does not release him. Patience relents, Jem is freed, and he goes away to get real help. Mary, meantime, at the shore, manages to slip away from those holding her, reaches the beacon, uncovers the light, pushes one of the thieves off a cliff. The ship is saved. Mary is captured and returned to the gang, Joss, knowing that the squire has a very very special interest in Mary, gets her on a cart and as he escapes the gang's revenge with her, is shot in the back.
Joss and Mary make it back to the Inn. Mary wants her aunt and uncle to escape to avoid the gallows, but Joss is too hurt, Patience is too much in love to leave him, so they wait too long. The Squire makes it back to the Inn, shoots Patience, and takes Mary hostage. The Squire has arranged his getaway with her on a ship that is about to sail. But Jem and others track him down after capturing the gang, and Jem rescues Mary from his grip. Mary is reconciled with Jem and it is clear an unlikely love has blossomed. The Squire is trapped on the ship, and goes up the highest mast to get away from those who are about to capture him. Rather than surrender, he jumps off the mast to his death.