A Gatherer's Adventure in Isekai follows the journey of Takeru Kamishiro, a thoroughly ordinary Japanese salaryman who finds his monotonous life abruptly ended. He is summoned by a mysterious divine being to the world of Madeus, a realm trapped in a destructive cycle of civilizational collapse. The god’s plan is to send an outsider with superior knowledge to act as a catalyst and break this endless loop. For his new life, Takeru is granted several powerful advantages: a supremely resilient body, immense magical potential, a "Search" ability to locate valuable resources, and an infinite storage bag.

Upon awakening near the humble Tormi Village, Takeru decides to work as a material gatherer, using his skills to collect herbs, ores, and monster parts, a profession that allows him to explore the new world at his own pace. His first major quest takes him to the Eastern Mountain to find Misril ore. There, he accidentally disturbs Voldius, an ancient and powerful dragon. Impressed by Takeru’s surprising magical strength, Voldius entrusts him with a task: to hatch a tainted dragon egg. By infusing the egg with his own magic, Takeru successfully hatches a baby dragon he names Bee, who becomes his constant and endearing travel companion.

The narrative is structured as a series of episodic adventures that follow Takeru and his growing party as they travel across Madeus. After leaving Tormi Village, his journey takes him to the large commercial city of Belkaim, where he becomes embroiled in local events, including helping to fend off a goblin attack. He develops a reputation for his unique gathering skills and willingness to help others, leading to a series of quests. These include seeking a rare ore for a blacksmith to forge a pair of special scissors, confronting a great demon that threatens an entire region, and finding a cure for a lord’s ailing wife, which requires obtaining a rare and dangerous flower.

As the series progresses, the focus expands to Takeru’s companions. He is joined by Brolite, an elf he rescues from exhaustion in the forest, and Hofvalpnir, affectionately called Pnir, a pegasus who becomes part of the group. A significant arc involves traveling to the sacred land of the elves, where it is revealed that Brolite is actually a high elf with a surprising and complicated personal history. Later, Takeru participates in a guild gathering competition, which tests his skills against other adventurers. The story continues to build towards encounters with powerful entities, including investigating the whereabouts of the elf-folk’s god and eventually meeting Luticara, Brolite’s older sister who has left her village.