Jonathan Osbourne, a decendant of Robert Louis Stevenson, observes his parents discover some old papers, then myteriously leave on a vacation to a deserted Atlantic island. When their plane is lost and Jonathan is forced to move in with a rich uncle, he becomes convinced that the papers are the key to their disappearance. His Uncle Pinchbeck, however, is suspiciously reluctant to discuss the papers, and insists that Jonathan stop worrying about the past and concentrate on his future at an elite private school.

Jonathan has no intention of giving up so easily. Together with his next-door neighbour, Katherine, he finds the missing papers on his uncle's private yacht. Thet reveal that the Treasure Island Robert Louis Stevenson wrote about was not fiction, and that his uncle has mysterious plans of his own for the island. There is even evidence that his parents may still be alive, stranded on the island. When his uncle's yacht is prepared for a long Atlantic voyage, Jonathan has no doubt about where it is headed.

Jonathan and Katherine stow away onto the yacht, and find that though Long John Silver is dead and gone, a new crew of modern pirates who work for his Uncle Pinchbeck have set their sights on recovering the remaining loot, and will stop at nothing to get it. There are storms, encounters with deadly wild animals, chases through the jungle, and on Jetskis, a secret industrial operation, and even the ghost of Flint makes an appearance.

No one will be quite the same after they Return to Treasure Island.