The story begins ten years after the appearance of a mysterious life form called Danpon, who created dungeons across the world. These dungeons yielded incredible discoveries: gourmet foods, magic stones as an alternative energy source, and miraculous medicines. Despite these advancements, daily life remained largely unchanged, with schools still operating as usual.
The narrative focuses on Yamamoto Touka, a transfer student from Yoshino, Nara, on her first day at a Dungeon Academy. Having overslept due to watching dungeon streams, she rushes to school and, after receiving directions from a silver-haired girl named Kagurazaka Kyou, finds her classroom. To her surprise, only two other students, Akemi Yukari and Higashi Sumire, are present. Touka's initial awkwardness is amplified when her classmates notice she's still holding her breakfast toast. Yukari, a gentle girl with wavy hair, and Sumire, a petite, serious girl with long hair, introduce themselves. Touka learns that her class, the Exploration Department, only has four students, and the entire first-year cohort consists of just six students, despite over a thousand applicants. Kyou, the girl who directed Touka earlier, is revealed to be her classmate. Kyou is an "Awakened," possessing magical abilities and distinctive silver hair, which she dislikes.
Their homeroom teacher, Kurenai Matsuru, announces that before the opening ceremony, they will visit the school's dungeon. This dungeon, unlike others, doesn't drop D-Coins but Magic Stones, which are converted into D-Points for use in the school's store or at graduation. Touka discovers her own status screen, showing her as Level 1 with basic stats and a "Status Ailment Resistance (Weak)" skill. Kyou, an Awakened, starts at Level 8 with magic.
The students are then led into the dungeon, where they are subjected to a terrifying ordeal. Kurenai-sensei paralyzes them and unleashes a Minotaurus. The students are seemingly crushed to death, but they reappear unharmed, realizing they were saved by "Substitute Bracelets" that nullify death once and teleport them to the lobby. This shocking "prank" was intended to instill a fear of death, as the academy's headmaster, Dumpuru, believes dungeons are places of life and death struggle. Dumpuru, a mysterious being who appeared months prior and created new dungeons, emphasizes that failure in dungeons should lead to death, and the bracelets are a last resort, with their activation resulting in expulsion and a ban from dungeons.
The students then begin their actual dungeon training. They learn about weapon types, with Touka choosing a spear, Yukari a sword, and Sumire a bow. Kyou, despite being an Awakened, chooses gauntlets, influenced by her father, a top-ranked explorer who abandoned his family. Touka, Yukari, and Sumire struggle against Walking Mushrooms in the second floor, but are saved by Kyou's overwhelming power against a group of Goblins.
Later, Touka, inspired by a streamer named Delta, decides to train early in the morning. She, Yukari, and Sumire meet Kyou, who has also been training early. Kyou agrees to accompany them to the second floor, despite their lower levels, to help them train. They face more Goblins, and Kyou effortlessly defeats them, revealing her immense strength.
The students' motivations for attending the academy are revealed: Sumire wants to become a strong explorer to protect her sister, who was nearly killed in a dungeon incident. Kyou seeks to understand what changed her father, a renowned explorer, leading him to abandon his family. Yukari, who loves slimes, hopes to find a connection to her deceased twin sister within the dungeon. Touka's reason is simpler: admiration for a famous explorer team.
The curriculum includes regular school subjects alongside dungeon training. Touka struggles with trigonometry, but Kyou patiently explains its importance. The students also learn about weapon skills and the importance of choosing a suitable weapon. Kyou's choice of gauntlets is revealed to be a connection to her father's fighting style.
The narrative highlights the students' growing bonds as they train together. Kyou, though initially aloof, shows a protective side, guiding them and even smiling. The students face challenges, including the risk of expulsion if they die after their bracelets are used, and the realization that the academy's dungeon is designed to be more challenging than standard ones. Touka, determined to catch up to Kyou, works hard, balancing her studies, part-time newspaper delivery job, and dungeon exploration, all while grappling with the harsh realities and unique opportunities of the Dungeon Academy.