When Matsukaze Tenma returns to Raimon, he finds out that all his teammates and friends aren't members of the Raimon Soccer Club, as it doesn't exist anymore. Alpha, a future assassin from El Dorado, an international organization hell-bent on erasing soccer, as soccer has become a fearsome weapon in the future.

Tenma is saved by Fei Rune and his companion Clark Wonderbot, who ''comes from 200 years later'' to help Tenma to protect soccer. After they fix the timeline to the original state, Raimon Soccer Club is back, but El Dorado keeps sending assassin teams to destroy Raimon Soccer Club, and so the team go on a quest to assemble The Strongest Eleven in History and collect their aura to strengthen themselves in order to defeat El Dorado.