It is 10 years after the events of Treasure Island and Jim Hawkins return home from the University of Oxford. Long John Silver also visits the Admiral Benbow Inn. He has his mind set on Flint's map because he knows the old pirate's diamonds are still on the island.
Jim Hawkins has been assigned to Squire Trelawney's plantation in Jamaica so he and his servant Ben Gunn set sail aboard the Saracen for the colonies. Amongst the prisoners in the ships hold is Long John Silver, who soon works his way up to ship's cook.
After surviving a mutiny on the Saracen, Hawkins, Silver, Gunn and several others find themselves on the mysterious island of Santa Anna. Apparently, in the past, only lunatics and undesirables were marooned by the Spaniards there.
Having finally arrived at his post in Jamaica, Jim Hawkins soon finds the bookkeeping at Trelawney's plantation to be out of order. He befriends a young slave named Abed but makes an enemy out of plantation manager Joshua Hallows.
Long John proposes to help Jim expose the corruption on the plantation in exchange for Flint's map. But when Hallows learns about the diamonds left on Treasure Island, he seeks out the map himself.
Silver leads Jim and his friend Van der Brecken to a pirate hideout known as The Crow's Nest. There Long John plans to muster up a new crew for the trip to Treasure Island.
Arriving in Mexico, Jim Hawins takes his leave from Van der Brecken and former slave Abed. But Conchita from the Crow's Nest follows Jim as he makes travels further on his own.
Hawkins and Silver finally return to Treasure Island with their new compatriots. But Joshua Hallows is already there, forcing his men to dig feverishly.