Isla Rune, a mysterious girl, who attended Raimon Junior High, decided to keep an eye on the football team, due to her interest in football. The school itself which gained its reputation after the amazing performance shown 10 years earlier in the Football Frontier International, a tournament that hosts the best youth teams the world has to offer. Unfortunately, the once renowned school doesn't have the football spirit it once enjoyed. This is primarily due to the fact that football in Japan is now controlled by a dark entity known as the 'Fifth Sector'. They alone decide the fate of every match, instructing teams to either win or lose. The actions of the Fifth Sector have beaten down the country's football teams, who no longer have a love for the game. Isla predicts that the team will come to realise what they truly wanted. And because of that, after the tournament, football's reputation returned. But not all happiness is permanent. After doing the education programme, Isla ran into Tenma, who told her everyone had lost interest and the love for football. They neither remember Tenma nor they have a recollection of how they competed in the Holy Road Tournament. As Tenma baffled by this twist, Alpha, the leader of the Route Agents and captain of Protocol Omega team, suddenly, appears before him. Alpha declares that he and his team are responsible for wiping out passion for football in Raimon, along with the memories of the football club members: and Tenma and Isla themselves were next. That's when a strange boy named Fei Rune appears just in time to save him. Just who is Fei? What connections does he have with Isla? And why does Alpha want to eliminate football for good? Tenma knows that he needs to do everything in his power to emerge victorious. It's a battle that could seal the fate of football forever.