Set against the "bleak and windy moors of Cornwall," the story follows a young, resilient protagonist named Mary. Following the death of her mother, Mary seeks refuge at Jamaica Inn, a place defined by its "cold and lonely" atmosphere. The inn is managed by her "scary and abusive Uncle Joss," a figure who immediately establishes a sense of dread for Mary, despite her aunt’s warnings to "stay out of his way."
Mary quickly discovers that Jamaica Inn possesses a "terrible reputation," which keeps legitimate travelers away. The tension escalates one Saturday night when a "noisy group of Joss's friends" arrives. Witnessing their rudeness, Mary observes suspicious activities from her bedroom window, including "horses and wagons moving in the yard" and her uncle violently assaulting a man. Her attempt to seek justice through the local magistrate, Squire Bassett, proves futile as he finds "nothing" during his investigation. Furthermore, when Mary confides in the local vicar, Mr. Davy, she is dismissively told that she "shouldn't involve the law."
Mary’s path crosses with Jem, Joss’s brother. Although initially suspicious, she eventually trusts him, only to have him disappear after a horse fair. Fearing for his safety, Mary discovers the true nature of Joss’s operation when she confronts him. She learns that the gang’s primary objective is to "wreck a ship and steal its cargo." The brutality of this enterprise is laid bare as Joss guides a ship "onto the rocks," callously allowing the sailors to "drown in the wild and dangerous water" while he and his men profit from the wreckage.
Following a violent confrontation among the gang members, Mary discovers the aftermath of the chaos: her uncle and aunt are found "murdered, lying on the cold stone floor." Seeking sanctuary, she turns to the vicar, Mr. Davy. In a chilling revelation, the vicar admits that he "controlled Joss's illegal activities" and orchestrated the murders to protect his own reputation.
As the vicar attempts to flee with Mary, they are stranded by a "thick fog on the moor." The arrival of a search party led by Jem brings a dramatic conclusion to the ordeal. Jem kills the vicar and rescues Mary, allowing for a profound realization: Mary has fallen in love with Jem. The narrative concludes on a hopeful note, with the couple planning a life "far away from Jamaica Inn," successfully escaping the dark, traumatic memories of the moorland pub.