The main character, Endou Mamoru, is a very talented goalkeeper and the grandson of one of the strongest goalkeepers in Japan, who died before he was born. Even though his skills are incredible his school lacks a real soccer club as the 6 other members don't appear very interested even in training. But as soon as a mysterious forward called Gouenji moves to Endou's town, the young goalkeeper sets out to find and recruit members for his soccer team.

Tenma Matsukaze, a first year who loves soccer, has exceptional dribbling skills, but still has lots of room for improvement. He enters Raimon Jr. High ten years after the first Football Frontier International, where Raimon has become famous for its soccer team. However, an organization called Fifth Sector has taken control of soccer over the years, and the passion that Raimon once had for soccer is no longer there.

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.

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?