The story is set after the end of Holy Road tournament finals of the first Inazuma Eleven GO anime, and Tenma returns to Raimon Junior High School. However, this is not the Raimon that Tenma remembers, and the members of the Raimon team no longer play soccer.
Tenma realizes that this is a parallel world when Alpha, the captain and forward of the Protocol Omega team, appears before him. Alpha is part of a secret project in the future to wipe out soccer.
To aid Tenma in his adventures, the Inazuma Caravan van seen in previous Inazuma Eleven anime has been modified into a flying time machine.