With the invention of anti-gravitational shoes known as Grav-Shoes, the ability to fly freely has become an everyday experience for the people inhabiting a four-island archipelago south of Japan. This invention has brought the people new ways of living and also a new sport known as Flying Circus, where participants gain points by either touching floating buoys or their opponent's back. The gullible and clumsy Asuka Kurashina, newly transferred to Kunahama High School, enters this world of flight unknowingly when she is able to pull off a difficult maneuver the first time she participates in a Flying Circus match. Eventually, this leads her to join her school’s Flying Circus club. Led by their coach, Masaya Hinata, their members consist of the experienced Misaki Tobisawa and her overprotective friend, Mashiro Arisaka. Ao no Kanata no Four Rhythm follows this rookie group soaring high above the skies and toward their dreams, armed only with their unwavering passion against an uncertain future.

Humanity finds itself in a struggle when the sea level begins to rise to an unprecedented level in the year 2039. To make matters worse, powerful enemies resembling old wartime vessels called the Fleet of Fog roam the waters, severing communication and transit to various regions. Any attempt at retaliation ends in failure with humanity's current weaponry. Only Gunzou Chihaya stands a chance against the Fleet of Fog as captain of the friendly Fog I-401 submarine Iona. As a result, Gunzou and his crew, known as Blue Steel, are tasked with a critical delivery mission by the Japanese government: they must deliver humanity's last hope against the Fleet of Fog, the Vibration Torpedo Warhead, through hostile waters to the United States for mass production. Though involved in the unsavory conflict, Blue Steel strives for nothing more than a peaceful resolution to it. As Iona undertakes the current mission and tasks beyond it, the crew upholds their values even in the face of harsh situations.