Jim Hawkins is a young orphan who lives in an inn in England with his best friends Gonzo and Rizzo. Jim listens to Billy Bones' tales about the pirate Captain Flint, who buried his treasure trove on a remote island and executed his crew so only he would own the island's map. One night, Bones' crewmate Blind Pew arrives, giving Bones the black spot. Just before dying of a heart attack, Bones gives Jim the treasure map and begs him to go after the treasure and keep it safe from pirate hands, especially a one-legged man. Just then, an army of pirates attack the inn, destroying it, but Jim, Gonzo, and Rizzo escape with the map.

The trio takes the map to the half-wit Squire Trelawney (Fozzie Bear), who arranges a voyage to find the treasure. The boys are enlisted aboard the Hispaniola as cabin boys, accompanied by Trelawney, Dr. Livesey (Bunsen Honeydew), and Beaker. The ship is commanded by Captain Abraham Smollett (Kermit the Frog) and his overly strict first mate, Mr. Arrow (Sam Eagle). The boys meet the cook Long John Silver, the one-legged man whom Bones warned them of, but Jim and Silver become good friends. The ship sets sail, but Smollett is suspicious of the crew, believing them to be of shady character. After Gonzo and Rizzo are kidnapped and tortured by three of the crew who have turned out to be pirates, he has the treasure map locked up for safe keeping.

It is revealed that Silver and the secret pirates in the crew had been part of Flint's crew and want the treasure for themselves. Silver fools Mr. Arrow into leaving the ship to test out a rowboat, says he drowned, and has his minions steal the map during Arrow's memorial service. Jim, Gonzo, and Rizzo discover Silver's treachery and inform Smollett. Arriving at Treasure Island, Smollett orders the entire crew save the officers to go ashore, planning to keep himself and non-pirate crew aboard the ship and abandon the pirates on the island. However, his plan falls through when it is discovered that Silver has kidnapped Jim to have leverage against the captain. On the island, Silver invites Jim to join them in the treasure hunt using his late father's compass. When Jim refuses, Silver forcibly takes the compass from him. Smollett, Gonzo, and Rizzo land on the island in an effort to rescue Jim. However, unbeknownst to them, Silver had hidden a squad of pirates aboard the Hispaniola before leaving, and they capture the ship in Smollett's absence. On the island, Smollett and the rest of the landing party are captured by the native tribe of pigs, where Smollett reunites with his jilted lover Benjamina Gunn (Miss Piggy), the tribe's queen.

The pirates find that the cave in which Flint hid the treasure is empty, leading to a brief mutiny against Silver. Silver reveals that, even though he is a pirate, he cares for Jim and allows him to escape. After reprimanding the crew from using a page from the Bible to deliver a death sentence, Silver and his crew capture Smollett and Benjamina. Smollett is hung from a cliff to fall to his death, joined soon by Benjamina after she reveals where the treasure is hidden to save his life. Jim rescues his friends and with an alive Mr. Arrow, who portrays his own ghost to scare the pirates aboard the ship, the group regains control of the Hispaniola and rescues Smollett and Benjamina.

The group engages the remaining pirates in a sword fight on the beach with Sweetums defecting to Smollett's side until only Silver is left standing, but he surrenders when he finds himself outnumbered. While the pirates are imprisoned, Silver discovers he still has Mr. Arrow's keys and tries to escape with the treasure during the night. Jim confronts him and threatens to give his position away, while Silver draws his pistol. In a tearful standoff, neither can bring themselves to follow their threats and Jim allows Silver to leave as long as they never cross paths again, much to their disappointment. Silver rows away, but not before returning Jim's compass to him and complimenting his kind heart. However, Mr. Arrow informs Jim and Smollett that the boat Silver used was not seaworthy, and Silver is later stranded on Treasure Island.

The crew of the Hispaniola sails away into the sunset, but not before some scuba-diving rat tourists recover the treasure from the sea.
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