Hidden in plain sight, spirits known as youkai inhabit the world. While most are benign, a certain subset threatens the tenuous peace between youkai and humanity. Ever since she agreed to become their God of Wisdom, Kotoko Iwanaga has served as a mediator between the two realms, resolving any supernatural problems that come her way. At a local hospital, Kotoko approaches Kurou Sakuragawa, a university student whose long-term relationship ended with an unfortunate breakup. Kotoko harbors feelings for him and suspects that something supernatural lurks within his harmless appearance, so she asks Kurou for his assistance in helping out youkai. Two years later, news of an idol who was accidentally crushed to death by steel beams flooded the press. However, months later, sightings begin to tell of a faceless woman who wields a steel beam. As is the case for any supernatural problem, Kotoko and her partner set out to stop this spirit from wreaking havoc—but this case may prove to be far more sinister and personal than they could have ever thought.

During a blizzard, Masayuki Muroi's old high school friend pushes him off a mountain to certain death. However, Masayuki survives the fall and escapes to safety thanks to Yuki-Onna, the spirit of a beautiful young woman who is said to lead men to their demise—but all she asks in return is money. Eleven years later, Masayuki has lived a successful life, having gotten married and amassing a great fortune. But when his company collapses and his wife cheats on him, Masayuki retreats to the city where Yuki-Onna once saved him, and he reconnects with her by offering her money and tasty meals. While Masayuki recovers from his misfortunes, another one knocks on his door: his ex-wife is found beaten to death, and now only Yuki-Onna—who cannot reveal herself—can corroborate his alibi. With no one to turn to, Yuki-Onna enlists the help of the spirits' God of Wisdom, Kotoko Iwanaga. Revered by the various spirits that wander the earth, Kotoko uses her extraordinary wits and cunning to solve all quarrels they may have. In her duty to protect spirits and humans from colliding, Kotoko drags along her immortal boyfriend, Kurou Sakuragawa, and promises to prove Masayuki's innocence without exposing Yuki-Onna's existence.

Distinguished mages Nanoha Takamachi, Fate Testarossa, and Hayate Yagami now work as military personnel for the Time-Space Administration Bureau on the planet Midchilda, having completed their studies on Earth in the last ten years since the Book of Darkness incident. One day, the three end up helping the Bureau respond to a severe airport fire, but their efforts are left unrecognized. A series of unfortunate events motivate Hayate to create the elite unit Riot Force 6, which handles cases involving public safety as well as dangerous magical objects known as Lost Logia. There the trio works alongside promising recruits Subaru Nakajima, Teana Lanster, Caro Ru Lushe, and Erio Mondial, who endure difficult training to fulfill expectations while overcoming hurdles and achieving personal goals. However, carrying out their mission proves to be a constant struggle. Battling foes who exploit the Lost Logia and facing criticisms from within the Bureau, Riot Force 6 quickly finds itself stretched thin.

In 2008, the Japanese government began hunting people who identify as otaku in an effort to protect the country's culture. In just one week, the enforcement agency known as the SSC captured almost every otaku by force and confiscated their memorabilia. One passionate man calling himself Otaku Hero refuses to allow this agency to do as they please: he raises a resistance army made up of other displaced geeks who band together to help defend their culture. Three years later, the fires of rebellion wane as all hope seems lost for otakus. Spurred on by his ally—the magical girl Anarchy—Otaku Hero commands the resistance in an effort to reunite Anarchy with the other two other magical girls: Blue and Pink. By combining the power of this trio, the resistance may be able to defeat the SSC and save otaku culture for everyone.