As a young boy from a noble family in Amawakuni, Arata has always expected to make life his own—until word of the princess growing weak reaches his city. Unbeknown to him, his grandmother had claimed him to be female at birth, and now, with no other girls to succeed the princess from the matriarchal Hime clan, he is next in line for the throne! Disguised as a woman awaiting a replacement to be found, Arata witnesses an assassination attempt on the princess by none other than her own guard, the 12 Shinsho. The crime is pinned on his head, forcing Arata to escape to the Kando forest, where it is said that no one comes out the same. Meanwhile, in modern-day Japan, Arata Hinohara longs for escape from the cruelty of his classmates. Hearing his name called from an alley, he wanders from his path and unwittingly switches universes with Arata from Amawakuni. With his own power as a newly awakened Sho—a warrior able to wield Hayagami, weapons with the power of the gods—and the help of his companions he meets along his journey, Hinohara sets out to restore order to this new world.

The ExWire of True Cross Academy are beset with shock and fear in the aftermath of discovering that one of their own classmates, Rin Okumura, is the son of Satan. But for the moment, they have more pressing concerns than that of Rin's parentage: the left eye of the Impure King, a powerful demon, has been stolen from the academy's Deep Keep. After an attempt is made to steal the right eye in Kyoto as well, Rin and the other ExWires are sent to investigate the mystery behind the Impure King and the ultimate goal of the thief. While this mission has them cooperating for the time being, Rin has never felt more distant from his fellow exorcists. In his attempt to reconcile with them, he undergoes specialized training to control his dark power. However, when the right eye is stolen not long after their arrival, the unthinkable threat of a traitor amongst them leaves them in need of all the power they can get.

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.