The story is set on Okinawa's isolated island of Iwado, which has seen a growing movement advocating a return to an autonomous government. Ao Fukai, a 12-year-old boy with a missing father, lives on the island with an old doctor named Toshio and is about to enter middle school. Ao's mother was taken away a decade ago by unknown individuals. Naru Arata, Ao's 12-year-old childhood friend and the story's heroine, lives with her father, older sister, and grandmother. She has a "Yuta" power awakened within her due to an incident when she was young. A mysterious entity called "Secret" suddenly appears and launches an attack on the Scub Coral lifeform on the island. Ao launches a certain military FP called "Nirvash" aboard a Japanese military transport in his fervent desire to protect the island. (Source: FUNimation)

On a sunny July day in the 41st year of the Shinka Era, Jirou Hitoyoshi is tasked with covertly listening in on a secret meeting between a top government scientist and an industrial spy. However, his cover is blown, and the spy reveals himself to be an alien in disguise. Amidst the ensuing chaos, Jirou enlists the aid of cafe waitress and magical girl Kikko Hoshino, one of many "superhumans" who blend into society and secretly protect humanity from extraterrestrial threats. As a member of the government agency known as the Super Population Research Laboratory, Jirou has the dual task of protecting superhumans that defend humanity and disposing of any deemed too dangerous to live. Having proven herself a worthy ally, Kikko is invited to join the agency as its newest recruit. Fast forward five years: disapproval and distaste for superhumans are now commonplace in Tokyo. From government corruption and conflicting ideas of justice, to the morality of superhuman rights, the relationship between humans and the supernatural minority balances precariously in a world pervaded by whispers of unrest and unease. Under mysterious circumstances, Jirou has betrayed the agency, and is now a fugitive on the run. As he skulks through the rainy back alleys of Shinjuku, he is pursued by the very same superhumans that he himself once recruited.

It is the dark century and the people are suffering under the rule of the devil, Vandel, who is able to manipulate monsters. The Vandel Busters are a group of people who hunt these devils, and among them, the Zenon Squad is known to be the strongest busters on the continent. A young boy, Beet, dreams of joining the Zenon Squad. However, one day, as a result of Beet's fault, the Zenon squad was defeated by the devil, Beltose. The five dying busters sacrificed their life power into their five weapons, Saiga. After giving their weapons to Beet, they passed away. Years have passed since then and the young Vandel Buster, Beet, begins his adventure to carry out the Zenon Squad's will to put an end to the dark century.

In an alternate universe, shy, awkward Yuki Nagato attempts to court her crush, Kyon, with the help of her best friend and neighbor, the perky and indomitable Ryoko Asakura. Together, the trio defends their high school literature club from extermination…and from the pestering of their over-the-top classmate Tsuruya and her friend and minion Mikuru. (Source: FUNimation, edited)