An ordinary Japanese salaryman, Takumi Iruma, is accidentally caught in a hero-summoning spell and transported to the fantasy world of Mildgard. Unable to return to Earth, the goddess Nolyn resurrects him as a 17-year-old and offers any skill as compensation. Hoping for a quiet, peaceful life, he chooses alchemy, only to discover it is an extraordinarily powerful ability allowing him to create almost anything, from holy swords to flying ships. Given a fresh start, Takumi aims to live modestly, but his unique inventions and growing power inevitably draw widespread attention.

The story takes place in Mildgard, a world of swords, magic, and political intrigue, where alchemy is a nearly forgotten art. Takumi initially settles in the city of Bolton, joining the Adventurer's Guild and creating a life for himself. His journey begins with a focus on small-scale crafting, such as inventing a magical toilet and producing luxury spider silk, which quickly establishes him as a successful merchant. His peaceful days change as he tames a powerful killer spider named Maple, who becomes a loyal companion and translator, and forms a party with a beautiful elf warrior, Sofia Sylphid, and his cheerful housekeeper, Maria. The group undertakes quests, defeats monsters like goblins and a Goblin General, and clears dungeons, all while Takumi levels up his skills and unlocks new magical abilities.

As Takumi's reputation grows, he attracts the attention of powerful figures. The Holy Sidonia Empire becomes interested in his purification magic devices, while the Kingdom of Barcula seeks his help with pioneering efforts. A key narrative arc involves Takumi moving to the Royal Capital, where he acquires a fox-eared slave girl named Reyva who shares his interest in alchemy, and later adds the rabbit-eared Máni to his growing household. The story escalates when it is revealed that Nolyn sent Takumi to Mildgard one year before three official heroes are summoned by the Holy Sidonia Empire for sinister purposes. This sets up a larger conflict between the goddess and the empire. The series concludes with a major battle where Takumi and his party, known as the Wings of Nolyn, defend their fortress town of Wedgefort from a massive monster horde, a direct consequence of the empire's hero summoning and the growing turmoil in the land.