Mamoru Endou is a cheerful goalkeeper in Raimon Jr High, with six other players in the team. But there was a day when the team was almost lead to disbandment by Natsumi unless they are able to win the match against the Teikoku Gakuen, currently the best team in Japan. He tried to save the club by gathering four more players to join the team.

Ares depicts an alternative canon following the events of the first season of the original Inazuma Eleven anime after their victory in the Football Frontier, with the alien attack from the second season never occurring. When Japanese soccer has been deemed weak compared to international competition, the Raimon Eleven disbanded with its members transferring into different soccer teams across the country to strengthen Japan's soccer at a national level. Furthermore, sponsorship has become a vital aspect in a Japanese youth soccer team's survival as it prevents a team's disbandment while being essential to partake in matches.

The series focuses on the forward Asuto Inamori and his team, Inakuni Raimon, which is made up of players from the remote Inakunijima Island. Needing to maintain their club, they have replaced the original Raimon Eleven as Raimon Junior High's soccer team and compete as underdogs in the annual Football Frontier youth tournament.