Endou Mamoru is a cheerful goalkeeper in Raimon Jr High, along with six other players in the team. But there was a day when the team was almost lead to disbandment by Raimon Natsumi, a daughter of the owner of the school,Raimon Souichirou. Unless they are to win the match against Teikoku Gakuen, currently the best team of Japan. He tries to save the club by gathering four more players to the team.

Matsukaze Tenma, along with the members of the Raimon team, now aim to free soccer so that everyone can finally play soccer freely without being ordered how to do it. The rebellion starts against Fifth Sector, in this dark midst of times, the Raimon team will not go alone in this rebellion. With some unexpected help from the Resistance organization that aims to replace the Holy Emperor and with some help from the previous main characters of the Inazuma Eleven anime.

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 is in a different club from Tenma. Is this a parallel world? Tenma wonders. That's when Alpha appears before him. Alpha wants to erase Tenma's passion for football.

In the final season of Inazuma Eleven Go Series, Football Frontier International Vision 2 (FFI V2) is being held, and all the best school soccer teams gathered in hope to gain a place in Shinsei Inazuma Japan, Japan's new national soccer team. But things are getting out of control when instead of skilled players, 8 soccer players who are new to soccer are selected, along with Tenma, Tsurugi and Shindō. The team is deemed to be a failure by both audience and Shindō himself, so what is happening? Will Shinsei Inazuma Japan be able to shine on the world stage, or is it too bad to even win a match?