In a world plagued by magical dangers and threats, there exist special warriors—known as Inquisitors—who are tasked with non-violently preventing these threats and nefarious actions. The Anti-Magic Academy is a specialized school built to educate and train these Inquisitors, which splits its students into small squads in order to train them to work together. Among these talented squads is the 35th Test Platoon, also known as the Small Fry Platoon due to its low ranking and incompetent members. However, everything changes when Ouka Ootori, a powerful yet rebellious former Inquisitor, is forced into joining due to her tendency to break rules and committing a serious violation: the killing of a witch. Tempers flare upon her arrival, as she clashes with their clumsy captain Takeru Kusanagi and argues with the rest of the squad over her views on witches. This eclectic group has a long way to go if they wish to succeed and climb the ranks at the Anti-Magic Academy: they must first set aside their differences and come to work together as a team.

Kimihiko Kimizuka has found himself inadvertently entangled in various crimes more times than he can remember, referring to himself as a magnet for trouble. One day, as if it was nothing out of the ordinary, a group of unknown men kidnaps him, forcing him to board a flight—where he also encounters a hijacking. Amid the resulting chaos, however, Kimizuka meets a stunning silver-haired beauty, going by the codename Siesta, who then saves the day. Claiming to be a legendary detective, Siesta enlists Kimizuka to be her sidekick. Though Kimizuka refuses at first, with Siesta's insistence, he eventually joins her—marking the start of a grand adventure spanning the entire world, preventing multiple threats that could spell doom for humanity along the way. Unfortunately, after three years of their unpredictable yet enjoyable time together, Siesta abruptly passes away. Distraught, Kimizuka tries to leave all memories of her behind, but as he begins to meet more people, it seems that Siesta's influence will never truly die.

With another Wave happening in a week, Naofumi Iwatani and his party have no time to waste. However, when bat familiars raid Lurolona Village and the Wave countdown comes to a halt, the Four Cardinal Heroes reconvene with the queen, Mirelia Q Melromarc, for a quick briefing. The queen presumes that the odd occurrences are linked to the Spirit Tortoise—a threatening creature that has awakened from its slumber, back to cause havoc once again. A plan to put the Spirit Tortoise to rest is devised—but out of the four men, only the cursed Shield Hero agrees to help.

The Four Cardinal Heroes are a group of ordinary men from modern-day Japan summoned to the kingdom of Melromarc to become its saviors. Melromarc is a country plagued by the Waves of Catastrophe that have repeatedly ravaged the land and brought disaster to its citizens for centuries. The four heroes are respectively bestowed a sword, spear, bow, and shield to vanquish these Waves. Naofumi Iwatani, an otaku, becomes cursed with the fate of being the Shield Hero. Armed with only a measly shield, Naofumi is belittled and ridiculed by his fellow heroes and the kingdom's people due to his weak offensive capabilities and lackluster personality. When the heroes are provided with resources and comrades to train with, Naofumi sets out with the only person willing to train alongside him, Malty Melromarc. He is soon betrayed by her, however, and becomes falsely accused of taking advantage of her. Naofumi then becomes heavily discriminated against and hated by the people of Melromarc for something he didn't do. With a raging storm of hurt and mistrust in his heart, Naofumi begins his journey of strengthening himself and his reputation. Further along however, the difficulty of being on his own sets in, so Naofumi buys a demi-human slave on the verge of death named Raphtalia to accompany him on his travels. As the Waves approach the kingdom, Naofumi and Raphtalia must fight for the survival of the kingdom and protect the people of Melromarc from their ill-fated future.