When Tomo Yamanobe's father—the former headmaster of Saint Mikhailov Academy—disappeared, he left nothing behind except for a piece of art called the icon. Soon after his disappearance, rumors of a serial killer attacking female students of the academy began to spread. As Tomo and her sister Mafuyu Oribe head home after being tormented at school, Tomo trips over an injured silver-haired boy who abruptly vanishes while being tended to. Mafuyu goes to look for him, only to discover that the church holding the icon is burning down. When she tries to save the painting, the rumored serial killer suddenly attacks her with a mysterious ability to control magnesium. Appearing out of nowhere, the silver-haired boy, who can control iron, rescues Mafuyu. Mafuyu finds out that the boy, named Alexander Nikolaevich Sasha Hell, is a qwaser—a being who is capable of controlling an element through the power of soma, received through the act of breastfeeding. Confused by the ordeal, Mafuyu attempts to move past it with little luck, as Sasha transfers to her class the next day. What will become of Tomo and Mafuyu's normal school life with the danger of other qwasers looming close to them?

Yuuta Hibiki wakes up in the room of Rikka Takarada and notices two things: he has no memories, and he can hear a mysterious voice calling his name from a nearby room. On further inspection, he finds a robot—which introduces itself as Hyper Agent Gridman—behind the screen of an old computer. Much to Yuuta's surprise, Rikka cannot hear Gridman, nor can she see the ominous monsters looming over a thick fog as it envelopes the town outside. Another giant monster materializes in the city and proceeds to wreak havoc. Amidst the confusion, Yuuta is once again drawn to the old computer and merges with Gridman. Suddenly, he appears in the middle of the battle and is forced to fight the monster. Together with Rikka and fellow classmate Shou Utsumi, Yuuta forms the Gridman Alliance to defeat the monsters plaguing the city and find whoever is responsible for their emergence.

Serial murders have recently plagued Inaba, with the police struggling to find any leads. Despite this, due to his parents going abroad for work, Yuu Narukami moves to the small town to live with his uncle for a year. He enrolls at Yasogami High School, where he meets and befriends Yousuke Hanamura, Chie Satonaka, and Yukiko Amagi. While hanging out together after school, the group fills Yuu in on the urban legend known as the Midnight Channel—a mysterious TV channel that only appears at midnight on rainy days while the viewer is alone. Curious about the claim, Yuu decides to tune in that night, only to see the next victim of the serial murders appear on the screen instead. He also finds himself being drawn into the TV, which intrigues his newfound friends enough to want to investigate. Yuu ends up falling into the world within the TV, which is blanketed by a thick fog and swarming with hostile creatures known as Shadows. Realizing that this world is somehow connected to the murders, the Investigation Team forms with the goal of uncovering the mystery behind the incidents.

The ability to create miracles is not just a supernatural phenomenon; it is a gift which manifests in a limited number of human beings. Minimum, or small miracles, are special powers that only selected people called Minimum Holders possess. The detective agency Yokohama Troubleshooting, or Hamatora for short, is composed of the Minimum Holder PI Duo, Nice and Murasaki. Their office is a lone table at Cafe Nowhere, where the pair and their coworkers await new clients. Suddenly, the jobs that they begin to receive seem to have strange connections to the serial killer whom their friend Art, a police officer, is searching for. The murder victims share a single similarity: they are all Minimum Holders. Nice and Murasaki, as holders themselves, are drawn to the case—but what exactly is the link between Nice and the one who orchestrates it all?