The plot is set in the mid-18th century, where an old sailor named Billy Bones 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". A former shipmate named Black Dog confronts Bones and they get into a fight, causing Black Dog to flee. A blind beggar named Pew then visits the inn, delivering a summons to Bones called "the black spot". Shortly thereafter, Bones suffers a stroke and dies. Pew and his accomplices attack the inn, but are routed by excise officers, and Pew is trampled to death. Jim and his mother escape with a mysterious packet from Bones' sea chest, which is found to contain a map of an 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 on Trelawney's schooner, the Hispaniola, under Captain Smollett and Jim forms a strong bond with the ship's one-legged cook, Long John Silver. The crew suffers 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...