Captain Bones tells Jim to open his sea chest for the map. As Jim searches the chest, Captain Bones clutches at his heart and dies.

Jim can hear the pirates coming for Captain Bones and the map. Jim hides just as the pirates arrive.

The pirates are angry that they can’t find the map that Jim had taken out of the chest. The pirates start arguing and then hear people arriving on horses to help the innkeepers. The pirates run away, leaving the blind pirate by himself. One of the horses tramples him, and he dies.

Jim shows the map to Dr. Livesey and Squire Trelawney. Trelawney says that he’ll outfit a ship and they will all go in search of the treasure with Jim as a cabin-boy. Dr. Livesey cautions the group to keep the treasure map and the reason for their voyage a secret.

We next see Jim in a tavern. He’s been sent there by Trelawney to ask the tavern’s landlord, Long John Silver, to come aboard as ship’s cook and bring along men as the crew. As he’s there, he sees one of the pirates that raided his mother’s inn. He tries to stop the pirate from leaving, but the pirate pulls a knife and lunges at him. Long John trips the pirate, saving Jim. Long John befriends Jim and they all ready themselves for the voyage.

The group is ready to set sail for the island in search of treasure. Squire Trelawney has hired Captain Smollett to captain the ship. Smollett is not happy that they are sailing for treasure and fears a mutiny from the crew because they have also somehow figured out that they are sailing for treasure.

The first mate, Mr. Arrow, is seen giving the deckhand Israel Hands orders multiple times. Israel Hands does not respect Mr. Arrow. During a storm, Mr. Arrow gets swept overboard, held only by the safety rope tied around his waist. Israel Hands looks around to make sure no one is watching. He shows Mr. Arrow his knife and his intention and then cuts the rope. Mr. Arrow vanishes overboard.

Since no one saw it happen, Captain Smollett promotes Israel Hands to the first mate position.

Dr. Livesey asks Jim to get him an apple. The barrel is nearly empty, and Jim must climb in to reach one. From inside the barrel, he hears Long John Silver approaching. He hears John talking with Israel Hands and another crew member. They are recruiting crew members to join their planned mutiny. They are waiting for the Captain to take them to the treasure, and when John gives the word, they will kill the Captain and the other English gentlemen.

Jim tells the Captain and the other English gentlemen about the pirates’ mutinous plot. The Captain asks Jim to go ashore with the pirates to gain as much information as he can.

On the island, we see Long John telling Jim to run off and explore and then giving an order to another pirate to kill one of the crew that hasn’t agreed to their mutiny. Jim runs off as he is told but sneaks back to spy on Long John. Long John tries to convince one of the other sailors to join the mutiny. When he refuses, Long John hits him with his crutch and then murders him with his knife.

Jim, stunned and appalled, can’t help but step forward out of hiding and confront Long John. Long John invites Jim to join his mutiny. Jim refuses and flees into the forest. Long John orders the other pirates to find Jim and kill him.

Elsewhere on the island, Jim runs into Ben Gunn, a sailor that was marooned on the island three years ago when his crew came to the island looking for Flint’s treasure. He tells Jim of a little boat he made that Jim can use.

Jim hears gunshots and the ship’s canon in the distance. He sees the doctor and squire rowing for shore, but the pirates are firing the ship’s canon at them. They get hit, and they swim for shore. The English gentlemen and Long John and the pirates are in a race to reach the stockade.

The English gentlemen make it to the stockade first and take up defensive positions. Jim manages to meet up with them in the middle of the firefight. Pirates attempt to enter the stockade, but the gentlemen shoot and kill them. They have the upper hand here, but they’ve lost control of the ship, which leaves them stranded.

Long John Silver enters to try to negotiate with the English gentlemen. If they give him the treasure map, he will leave them food and supplies and send the first ship they see to come and pick them up. Captain Smollett rejects and gives him a counteroffer. If the pirates surrender, Smollett will take them home to a fair trial rather than killing them. Long John exits swearing that the pirates will overcome them before the hour’s up.

Captain Smollett deliberately angered Long John to get him to attack right away before they run short of food and water. He instructs everyone to stay vigilant and gives Jim a pistol with one shot in it. Captain Smollett gets shot but keeps fighting. Another one of the gentlemen gets shot and dies. Holding back tears of anger, Jim runs off to go get Ben Gunn’s boat.

We next see Israel Hands on the deck of the ship imagining that he is the captain. Jim cuts the ship’s anchor and climbs aboard. Jim tells him that he’s taking back the ship. He orders Israel to steer the boat to the beach. Israel starts to get the boat going in the right direction. He asks Jim to hold the wheel while he tightens a sail, but instead of working on the sail, he sneaks behind Jim about to kill him with his blade. Jim turns around just in time and tries to shoot Israel with his pistol. It misfires because it got wet. Israel runs after Jim with his knife trying to kill him. During their fight, the ship lands on the beach. Jim climbs up one of the masts with Israel following behind him. Jim manages to dry his pistol and reprime it. He fires, and Israel, shot from point blank range, falls overboard dead. Both triumphant and sick to his heart, Jim leaves the ship there for the gentlemen to come to when they’ve defeated the pirates.

It’s nighttime when Jim makes it to the stockade. The English gentlemen aren’t there, and he stumbles upon the pirates. Long John tells him that the English gentlemen surrendered because they saw that the ship was no longer anchored where they left it. They bargained for their lives in exchange for the treasure map and the stockade. Jim tells them that he was the one who spoiled their plan, cut the ship free from its anchor, and killed Israel Hands. The pirates want to kill him, but Long John stops them, moved by Jim’s courage. The pirates decide that Long John should no longer be their captain. He makes a deal with Jim that they will have each other’s backs and watch out for each other.

Long John shows the pirates that he has the map, and they agree to make him captain again. Long John shares that he had decided to spare the Doctor so they would have someone to take care of them. The Doctor enters, and Long John allows Jim and the Doctor to talk privately. Jim tells the Doctor that he has taken back the ship. The Doctor encourages him to run and escape, but Jim doesn’t want to break his agreement with Long John.

The pirates are off to follow the map and find the treasure with Jim in tow. They stumble upon a skeleton partially buried in the ground. They then hear a voice that sounds like the dead Captain Flint. The pirates are spooked, but then Long John notices a shadow, so it must be a living person trying to scare them. They make their way to the spot where the treasure should be, but there’s just an empty hole. Someone has been there before them! The pirates are furious and turn on Long John and Jim. They threaten to kill them when shots fire from the trees around them. One of the pirates falls and the rest flee.

The English gentlemen with Ben Gunn emerge from the trees. The pirate that fell raises his pistol and aims at Jim. Long John shoots him dead, saving Jim. Long John surrenders his weapons to the gentlemen. Ben Gunn shares that he had found the treasure a year ago. He moved it all to the entrance of a high cave so that it would glow when the sun hit it. He hoped that a ship would see it and come to rescue him. The sun shines on the treasure, and they are bathed in a golden light.

We next see the ship with its sails hoisted and ready to sail. The remaining pirates run after it begging to be taken with. They realize that they are being marooned on the island.

They have sailed the ship to an island port city to pick up supplies and find a new crew. Jim is left on the ship with Ben Gunn and Long John who is chained to the mast. To honor their agreement, Jim sets Long John free. Long John thanks him, and Jim says that if he ever hears that Long John is in England, he will see him hang. Long John leaves the ship a free man. Ben asks Jim what he’ll do with his share of the treasure. Jim plans to make sure his mother is well taken care of, and then he will buy a ship of his own and sail all over the world. Ben tells him it has been an honor to know him and tells Jim that he is a man now.