Hajime Nagumo, an ordinary high school student, is transported to a fantasy world alongside his classmates as part of a summoning ritual to aid in humanity's battle against demons. While most of his peers receive powerful combat abilities, Hajime is granted the seemingly mundane skill of transmutation, which allows him to manipulate materials. This perceived weakness leads to ridicule and isolation from his classmates, who quickly adapt to their new roles as heroes. During a dungeon exploration mission, Hajime is betrayed and left for dead by a classmate, falling into the depths of a treacherous labyrinth.

In the labyrinth, Hajime faces near-fatal encounters with monstrous creatures, but through sheer determination and ingenuity, he survives and begins to evolve. Using his transmutation ability, he crafts powerful weapons and armor, gradually transforming himself into a formidable fighter. Along the way, he forms a bond with Yue, a vampire princess imprisoned in the dungeon. Yue becomes his first ally and romantic interest, and together they escape the labyrinth, now stronger and more determined to survive in the harsh world.

As Hajime and Yue journey through the fantasy world, they encounter other companions, including Shea, a rabbit-eared beastman with immense physical strength, and Tio, a dragon with a penchant for masochistic humor. Each character brings unique abilities and perspectives, contributing to the group's dynamic. Hajime's primary goal shifts from mere survival to finding a way to return to his original world, a quest that becomes increasingly complex as he uncovers the darker truths behind the summoning ritual and the war between humans and demons.

The narrative explores themes of betrayal, resilience, and the moral ambiguity of power. Hajime's transformation from a weak and ostracized individual to a ruthless and pragmatic survivor is central to the story. His relationships with his companions, particularly Yue, provide emotional depth, balancing the series' action-heavy sequences. The plot delves into the political and social structures of the fantasy world, revealing the manipulative forces at play and the sacrifices required to challenge them.

Throughout the series, Hajime and his allies face numerous adversaries, including powerful demons, rival adventurers, and corrupt human factions. Their journey is marked by intense battles, strategic planning, and moments of camaraderie. The story also examines the consequences of Hajime's growing power, as his methods and decisions often blur the line between heroism and villainy. By the end of the series, Hajime's quest for a way home remains unresolved, leaving room for further exploration of the world and its conflicts.