Otaku siblings Tamotsu and Niwaka Denkigai are shopping in Akihabara when it is overrun by vampiric cosplaying monsters! These creatures, known as "Bugged Ones," can possess anyone they bite and soon they begin causing mayhem across the city. As Tamotsu finds himself at the mercy of one of these creatures, he is rescued by the mysterious baseball bat-wielding Matome Mayonaka. Together, they fight through several more encounters with the Bugged Ones, but before long, Tamotsu is fatally wounded protecting Matome. With no other choice, she revives him as a high level Bugged One—just like her! Tamotsu and Matome, along with excitable otaku cosplayer Arisa Ahokainen, make up the group "The Electric Mayonnaise" and they begin dispatching the Bugged Ones in the only way they know how: by ripping off their clothes and exposing them to sunlight!

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.

Abandoned as a child by her mother, Aoi Tsubaki has always had the ability to see "ayakashi"—spirits from the Hidden Realm. Shirou Tsubaki, her grandfather who shared the same ability, took her under his wing and taught her how to live with the ayakashi in peace. When her grandfather abruptly passes away, the independent Aoi must continue her college career, armed with only her knowledge in cooking as a means of protection against the human-eating spirits. In hopes that the ayakashi will not turn to her or other unknowing humans as a tasty meal, she takes it upon herself to feed the hungry creatures that cross her path. After giving a mysterious ayakashi her lunch, Aoi is transported to the Hidden Realm, where the ayakashi reveals himself to be an ogre-god known as Oodanna, the "Master Innkeeper." There, she learns that she was used as collateral for her grandfather's debt of one hundred million yen, and that she must pay the price for her grandfather's careless decision by marrying Oodanna. Aoi valiantly refuses and decides to settle things on her own terms: she will pay off the debt herself by opening an eatery at Oodanna's inn. Kakuriyo no Yadomeshi follows the journey of Aoi as she proceeds to change and touch the lives of the ayakashi through the one weapon she has against them—her delicious cooking.

In the year 2041, World War III has wiped out two-thirds of the human population, and in the newfound structure, the belief in any god or beyond-human entity is considered a preposterous notion. In order to prevent citizens from bearing possibly incriminating thoughts, the government has assembled a Special Weapon Enforcement division to capture and rehabilitate such believers. The Kirihara brothers, Naoya and Naoto—who were hidden away from society by their captors for years to conceal their psychic abilities—were promised freedom once the world was ready to face their existence. Now, wandering in the appalling new societal climate where psychics are not welcome, the brothers find themselves on the run from the Enforcement's devoted operatives, Yuuya and Takuya Kuroki.