After a soccer game, six kids are playing a cute RPG-like video game at home. One of them scored the winning goal, one was the goalkeeper who just missed the ball, and the others formed two pairs cheering for their respective teams. When they defeat a boss, a strange thing appears in front of them, and they get pulled into the game world! Tomoru (the scorer), Mio, and Dai end up together with Professor Galileo, who explains that he created the game they've entered, called Eureka, but got accidentally sucked in as well. To return to their world, they need to clear missions that appear in certain areas. So when a mission pops up, Tomoru and the group make the professor take them along.
Arriving at area C-1, they discover not only a mission but also a rival group! The rival professor has brought their opponents from the soccer game—Yukio, Suzuka, and Kouta—with him! The mission is scientific: first, the computer explains how lightning forms, and then they must figure out how to stop the lightning to clear it. Tomoru and company succeed, earning a Eureka Stone, which allows them to go back to their world—except the gateway actually requires ten Eureka Stones total before it will open. Looks like there's plenty of science to learn and missions to complete before they can go home.