In the mid-18th century, an old sailor who identifies himself as "The Captain" starts to lodge at the rural Admiral Benbow Inn on England's Bristol Channel. He tells the innkeeper's son, Jim Hawkins, to keep a lookout for "a one-legged seafaring man". Black Dog, a sailor, recognizes the captain as his former shipmate Billy Bones, and confronts him. They get into a sword fight; Black Dog flees, and Bones suffers a stroke. That night, Jim's father dies. Days later, Pew, a blind beggar, visits the inn, delivering a summons to Bones called "the black spot". Shortly thereafter, Bones suffers another stroke and dies. Pew and his accomplices attack the inn but are attacked and routed by mounted excise officers, and Pew is trampled to death by one of their horses. Jim and his mother escape with a packet from The Captain's sea chest, which is found to contain a map of the island on which the infamous pirate Captain Flint hid his treasure. Jim shows the map to the local physician Dr. Livesey and the squire John Trelawney, and they decide to make an expedition to the island, with Jim serving as a cabin boy.
They set sail from Bristol on a schooner chartered by Trelawney, the Hispaniola, under Captain Smollett. Jim forms a strong bond with the ship's one-legged cook, Long John Silver. The crew suffers a tragedy when first mate Mr. Arrow, a drunkard, is washed overboard during a storm. While hidden in an apple barrel, Jim overhears a conversation among the Hispaniola's crew which reveals that many of them are pirates who had served on Captain Flint's ship, the Walrus, with Silver leading them. They plan to mutiny after the salvage of the treasure, and to murder the captain and the few remaining loyal crew. Jim secretly informs Captain Smollet, Trelawney, and Livesey.
Arriving at the island and going ashore, Jim flees into the woods after witnessing Silver murder a sailor. He meets a marooned pirate named Ben Gunn, who is also a former member of Flint's crew. The mutineers arm themselves and take the ship, while Jim and Smollett's loyal band take refuge in an abandoned stockade on the island. After a brief truce, the mutineers attack the stockade, with casualties on both sides of the battle. Jim makes his way to the Hispaniola and cuts the ship from its anchor, drifting it along the ebb tide. He boards the ship and encounters the pirate Israel Hands, who had been injured in a drunken dispute with one of his companions. Hands helps Jim beach the schooner in the northern bay, then attempts to kill Jim with a knife, but Jim shoots him dead with two pistols.
Jim goes ashore and returns to the stockade, where he is horrified to find only Silver and the pirates. Silver tells Jim that when everyone found the ship was gone, Captain Smollett's party had agreed to a truce whereby the pirates take the map and allow the besieged party to leave. In the morning, Livesey arrives to treat the wounded and sick pirates, and tells Silver to look out for trouble once he's found the site of the treasure. After a dispute over leadership, Silver and the others set out with the map, taking Jim along as a hostage. They find a skeleton with its arms oriented toward the treasure, unnerving the party. Ben Gunn shouts Captain Flint's last words from the forest, making the superstitious pirates believe that Flint's ghost is haunting the island. They eventually find a treasure cache, but it is empty. The pirates prepare to kill Silver and Jim, but they are driven off by the doctor's party, including Gunn. Livesey explains that Gunn had already found the bulk of the treasure and taken it to his cave, long ago. The expedition members load this portion of the treasure onto the Hispaniola and depart the island, with Silver as their only prisoner. At their first port, in Spanish America, Silver steals a bag of money and escapes. The remaining crew sail back to Bristol and divide up the treasure. Some treasure was never found, but Jim refuses to return to the "accursed" island to look for it.
