Inazuma Eleven Go: Chrono Stone follows the Holy Road Soccer Tournament. The current hero, Tenma Matsukaze, has journeyed across Japan spreading the love of soccer to children.
After finishing his assignment he returns to Raimon Junior High, only to discover the school has changed. The soccer club is gone, and those who once formed the champion squad of the Holy Road Tournament have no memory of playing or even of Tenma. Confused, he is confronted by Alpha, the Route Agents" leader and captain of Protocol Omega, who claims responsibility for erasing both passion for soccer at Raimon and the memories of its players. Alpha now targets Tenma.
At that moment a mysterious boy named Fei Rune steps in to rescue him. Who is Fei, and why does Alpha seek to eradicate soccer entirely? Tenma realizes he must fight with all his might. The outcome could decide the future of soccer forever.