Chrono Stone takes place after the Holy Road Soccer Tournament. Tenma Matsukaze, the protagonist, made it his mission to impart soccer knowledge to children across Japan. Upon his return to Raimon Junior High School, he discovers that the school has changed beyond recognition. The soccer club has vanished, and the champion team from the previous tournament has no recollection of playing soccer, nor of Tenma. Alpha, captain of the Protocol Omega team and leader of the Route Agents, makes a sudden appearance before Tenma and claims responsibility for causing this memory loss. Alpha plans to eliminate soccer from Raimon permanently, with Tenma next on the list. A boy called Fei Rune rescues Tenma from Alpha's clutches. Tenma understands that he must do whatever it takes to save soccer from its fate. The outcome of this battle could determine the future of soccer worldwide.