The story begins with Watari Shinjo, a cynical and unmotivated high school student, caught in a violent earthquake. The classroom is plunged into inexplicable darkness, and upon investigation, Watari discovers the windows are sealed by artificial stone walls, and the corridor outside has transformed into a torch-lit dungeon passage. He hypothesizes they've been teleported into a supernatural phenomenon or a realistic dream. His initial fear gives way to a cynical acceptance of his likely death, but then a pragmatic desire to survive takes over.
Watari, accompanied by his timid but intelligent friend Midori Seki, begins exploring. They soon encounter Kumiko Kujo, a beautiful, high-achieving student council vice-representative from Class A, whom Watari secretly calls "Virgin Bitch" due to a past, complicated encounter where he tried to comfort her after she was rejected by another student, leading to her persistent, aggressive advances. Kumiko, despite her refined exterior, is revealed to be highly competitive and sexually forward with Watari.
The group, joined by other Class A students led by the charismatic Shuichi Nanami and his calculating aide Tsukasa Jinguji ("Insidious Glasses"), discovers lethal traps and encounters monsters: pig-faced Orcs and smaller Goblins. Naotsugu Mikami, a kendo champion, single-handedly dispatches an Orc, while Watari, Kumiko, and Seki also engage in combat, quickly adapting to the brutal reality of killing. Casualties mount rapidly, with several students dying from traps and monster attacks, including Mando Aya, whose death deeply traumatizes her friend Sashiki Ena. Jinguji is observed subtly manipulating weaker students to serve as trap-fodder, a tactic Watari finds abhorrent but understands as pragmatically effective for group survival.
A student named Ryuji Mikagami ("Mop-head") recognizes their predicament: they are trapped in "Genocide Reality" (Genoria), an old, notoriously difficult 3D dungeon RPG. Watari, a hardcore retro gamer, confirms this internally, realizing his extensive game knowledge is now a powerful "cheat." He decides to keep this knowledge mostly to himself to gain an advantage.
They reach a "city," a safe zone within the dungeon, but it's an underground, uninhabited medieval-style settlement with a glass ceiling. Watari uses his game knowledge to safely retrieve hidden treasure, acquiring gold and gems (which double as mana potions). He and Seki use the Oracle to determine their professions: Watari is a "Middle Fighter," and Seki is a "Priest." Kumiko reveals she is a "Lower Ninja," a rare, high-tier class. Watari teaches Seki and Kumiko how to craft potions and train their combat ranks by repeatedly attacking a steel wall, emphasizing the importance of both physical and magical development for survival.
A sudden "Dungeon Invasion" occurs, with a powerful "Mustard Dragon" (a 6th-floor monster) attacking the remaining students and teachers in the dungeon. Watari, despite his cynical nature, decides to help, partly swayed by Seki's concern and partly to maintain some order. He confronts the dragon, using his agility and knowledge of its weaknesses (slow turning, no side attacks) to slowly wear it down. Nanami and other students join the fight, and they eventually defeat the dragon, but not before most of the remaining students and all the teachers are killed by its poisonous breath. Watari is struck by the literal meaning of "Genocide Reality."
In the aftermath, Watari discovers that Health Potions can cure congenital disabilities when he gives one to Kazuha Rindo, a quiet, modest girl from his class with a leg disability, who is also Nanami's childhood friend. Nanami's protective stance towards Kazuha hints at his feelings for her.
Leaving Seki and Kumiko to continue training in the city, Watari descends deeper into the dungeon alone. He rapidly power-levels, defeating the Orc Lord (1st floor boss) and Kobold Lord (2nd floor boss) using strategic tactics and exploiting dungeon mechanics. He trains his physical abilities by repeatedly fighting "Rock Piles" and healing with potions. Using a "Rank Up Scroll" found after defeating the Kobold Lord, Watari ascends to the "Samurai Swordsman" class, a powerful, magic-attuned warrior. Now a formidable adventurer, Watari embraces his new reality, eager to explore the dungeon's depths with his newfound power.
