Following the end of the Holy Road soccer tournament, Matsukaze Tenma returns to Raimon Junior High after a break, only to find out that all of his friends and teammates no longer play soccer, and the soccer club apparently doesn't exist. He is soon after approached by a mysterious person called Alpha who reveals himself to be a time traveler (from an organization in the future known as El Dorado) on a mission to destroy soccer.

Together with the help of Fey Rune, Tenma must travel through time and save soccer before El Dorado rids the world of it forever.