The story is an adventure on the high seas and on the faraway Mollusk Island. An orphan boy named Peter and his mysterious new friend, Molly, overcome bands of pirates and thieves in their quest to keep a magical secret safe and save the world from evil. Villains include the scary but somehow familiar pirate captain “Black Stache” and the ferocious crocodile Mister Grin.
Molly and Peter take a voyage with Alf, James, Thomas, Prentiss, Tubby Ted, Slank and Little Richard from a filthy, crime-ridden port in Old England across the turbulent sea. Aboard the Never Land is a trunk that holds the “greatest treasure on earth,” thought by its pursuers to be gold or jewels but revealed to be “starstuff,” an alien chemical element (delivered to Earth by meteor strikes) that can either give people and animals magic powers, or kill them, depending on the dosage and other factors. The trunk is moved from place to place through storms and sea battles: once in a dry, guarded cabin, next in a ship full of greedy pirates, and then out in the open sea.
While on the ship, both Peter and Molly become close as they take on Slank and many other villains, including pirates. While they try to keep the starstuff out of the wrong hands, the Never Land shipwrecks and Molly saves Peter from death, and they fly for an unknown island.
When the shipwreck led them to a mysterious island, known as Mollusk Island, Molly is kidnapped by Slank and Peter saves her from him, along with the help of James, Thomas, Prentiss, and Tubby Ted who all go by the gang name, The Lost Boys. Peter also does battle against Black Stache and cuts off his hand with a sword; the amputee pirate will adopt the moniker “Captain Hook“. The book ends with Molly and Peter saying goodbye to each other and with Peter promising to visit her in England. Molly and her father, Lord Leonard Aster, return to the real world, while Peter and the Lost Boys remain on Mollusk Island, which they rename “Neverland,” the name of the ship that was shipwrecked. (However, the sequels still call the island Mollusk Island more often than Neverland.)