In Marvelous: Mōhitotsu no Takarajima, the famous pirate Captain Maverick is said to have left behind a great treasure known as the "Marvelous." The treasure is said to be protected by unsolvable puzzles and bizarre creatures. While many have gone looking for this treasure, none have ever returned. Now, a group of children on a field trip have landed on the island rumored to house the treasure, as did a group of pirates trying to get the treasure at all costs.

The game focuses on a group of three 12-year-old boys, Dion, Max, and Jack. Their teacher, Ms. Gina, helps them by giving them items to help organize their group. The game, influenced by The Legend of Zelda: A Link to the Past, is played by interacting with other characters and things. When the player encounters someone or something, a command window shows up with choices of how the player wants to interact with them.