After a soccer match one day, six children are playing a cute RPG-like video game at their homes. One of them scored the winning goal, another was the goalkeeper who just missed the ball, and the others were two pairs rooting for opposite sides. Suddenly, when they defeat a boss, a strange object 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 tells them he created the game they've entered, called Eureka, but he accidentally got sucked in as well. To return to their world, they need to clear missions that appear in certain areas of the world. So when a mission shows up, Tomoru and the gang make the professor take them along.
When they reach 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! Their mission is, of course, scientific. First, the computer explains how lightning forms, and then they must figure out a way to stop the lightning to clear the mission! Tomoru and company manage to accomplish it and obtain a Eureka Stone, allowing them to return to their world! Except... the gateway back actually requires ten Eureka Stones total before it will open! Sounds like there's plenty of science to learn and missions to complete before they can go home.