The story is told by Jim Hawkins, who looks back on the events at his family's Admiral Benbow inn, where an old buccaneer called Billy Bones takes lodging and drinks himself toward death in fear of a one-legged seafaring man. When Bones dies and pirates raid the inn, Jim and his mother save from the dead man's sea-chest a packet that proves to be the map to Captain Flint's buried treasure.
Jim carries the map to Squire Trelawney and Dr. Livesey, who fit out the schooner Hispaniola and take Jim along as cabin-boy. The squire, talking too freely in Bristol, lets the crew be stocked largely by the ship's cook, Long John Silver, a tall, smiling, intelligent man whose easy good humor wins everyone over and disarms Jim's early suspicion of any one-legged sailor.
Hidden in an apple barrel late in the voyage, Jim overhears Silver coaching a young hand into piracy and learns that most of the crew are Flint's old men planning mutiny once the treasure is found. He warns the captain, the doctor, and the squire, and the loyal few brace for a fight that breaks out as soon as the island is reached, with the honest party taking shelter in an old stockade.
Jim repeatedly acts on his own initiative, for better and worse. He slips ashore and meets Ben Gunn, a half-crazed castaway marooned three years by Flint's crew; later he cuts the anchored ship adrift, boards it alone, and in a deadly struggle is forced to shoot the treacherous coxswain Israel Hands. Returning to the stockade, he walks straight into the pirates' hands and finds Silver now holding him hostage.
Silver, reading the shifting odds, secretly allies himself with the doctor's party while still leading the pirates to the treasure, only to find the cache already emptied by Ben Gunn. The mutiny collapses, the worst pirates are killed or marooned, and the gold is shipped home. Silver escapes at a port with a bag of coin, and Jim closes by swearing that nothing would draw him back to that accursed island, whose worst dreams still wake him with Flint's parrot shrieking for pieces of eight.