When soccer comes under threat by a shady organization from the future, Tenma and his team traverse through time to stop the eradication of soccer from history.

The story begins with following Raimon's success on the Holy Road soccer tournament. Tenma returns to Raimon Junior High, but finds out that things have changed. The Raimon members are not soccer players anymore. In fact, there is no soccer club at the school. Shinsuke and the others are in a different club from Tenma. Is this a parallel world? Tenma wonders. That's when Alpha appears before him. The organisation called El Dorado is an organisation formed by the future world's countries to deal with important matters of world affairs, and for some reason, they've determined that soccer must be destroyed. To do so, they have assigned Alpha and his team, Protocol Omega to the mission of ridding soccer from the world.—Inazuma Eleven Wiki