The story revolves around Mike Jones, a star pitcher from Seattle, who comes to C-Island to visit his uncle, an archaeologist named Dr. Steve Jones, after receiving a letter from him. Uniquely, this letter was actually packaged with the game and addressed to the player. Just as Mike carries the letter inside the game, so too must the player keep it for later use. During his visit, Mike discovers that his uncle has been abducted by aliens. Wielding an island yo-yo, Mike travels from isle to isle in a submarine piloted by an AI named NAV-COM (short for Navigational Computer) and fights his way through caves searching for clues to his uncles capture.