The story begins with Nanami Akihiko, a towering high school freshman, performing his duty as a student council member during the morning greeting campaign. Despite his intimidating 201cm stature and muscular build, Akihiko is a kind and polite individual, though his appearance often frightens his peers. He is accompanied by his two close friends: Kenji Emiya, an enthusiastic idol otaku, and Yuta Isurugi, a gentle and physically frail boy who has been a target of bullying since elementary school. Yuta confides in Akihiko that he is being troubled, hinting at a recurring issue.
Later that day, while conducting a post-school patrol, Akihiko hears suspicious noises from an unused classroom. He bursts in to find Yuta, injured and partially undressed, being harassed by a group of delinquents led by a larger man wielding a metal bat. Akihiko, despite being outnumbered and initially taking a blow, quickly incapacitates the leader with his karate skills. The delinquents are then given a choice between calling the police or facing disciplinary action, leading to their surrender.
As Akihiko and Yuta walk home, a strange, warm wind blows, and a large, glowing hole, resembling a cave entrance, suddenly appears beside them. Despite the unnatural and eerie nature of the phenomenon, both boys feel an inexplicable urge to enter, sensing the beginning of an adventure. Inside, they discover a fantastical space illuminated by glowing moss and minerals. They stumble upon a shoulder bag that impossibly contains a spear, seven thick books, a shield, a staff, and four flasks of green liquid.
Their exploration is interrupted by the appearance of giant ants, each the size of a puppy. Akihiko attempts to fight them using his martial arts, but his human-centric training proves ineffective against the monstrous creatures. During the fight, Yuta, remembering the items from the bag, uses the shield to deliver a decisive blow to one of the ants, surprising Akihiko with his newfound courage.
As they venture deeper, they encounter more monsters, including moss balls and larger ants. They eventually find a wooden door leading to a small room where they meet a woman named Rizon. Rizon reveals that the cave is a "dungeon," a place that has suddenly appeared worldwide, and that the items they found are hers. She heals their injuries and explains that they have the potential to become "magic users." Rizon gives them the "dungeon watch," a device that displays their stats and allows them to use "dungeon points" (DP) earned from clearing dungeons to improve their abilities and learn skills.
Akihiko discovers he has a rare "null attribute" magic, while Yuta excels in fire, wind, and light magic. They learn that dungeons pose a threat if left unchecked, as monsters can "flood" into the outside world. Rizon tasks them with clearing dungeons to become stronger and promises to reveal more about their world's new reality once they conquer intermediate dungeons.
The boys return to the dungeon the next day, now equipped with weapons and a better understanding of their abilities. They fight through monsters with increased efficiency, their physical and magical capabilities significantly enhanced. They discover that the green liquid in the flasks are "magic potions" that restore health and magic. After reaching the boss room, they face a giant, one-eyed spider. Through teamwork, Akihiko's strategic thinking and Yuta's magic, they defeat the boss.
Upon clearing the dungeon, they receive a massive amount of DP and are recognized for their achievements. Rizon reappears, explaining the function of the dungeon watch, including its "DP shop" where they can purchase stat boosts and skills. Akihiko buys spear skills, while Yuta focuses on magic efficiency and physical enhancements. They also learn about the "Library" function, which records information about monsters and items, and the "Dungeon Search" function, which shows the locations of other dungeons and warns of potential "floods." The story concludes with Akihiko and Yuta resolving to become stronger and explore more dungeons, driven by the desire to protect their world and uncover the truth behind the emergence of dungeons and magic.