The manga "Herbivorous Dragon of 5,000 Years Gets Unfairly Villainized" centers on a peaceful, herbivorous dragon who has lived for millennia without causing harm to humans or other creatures. Despite his gentle nature, the dragon is unjustly labeled as a fearsome villain by humans who misunderstand his intentions. This misconception arises from a series of misunderstandings and exaggerated legends that paint him as a malevolent force. The dragon, who prefers solitude and a quiet life, finds himself constantly pursued by adventurers, knights, and other individuals seeking glory by defeating him.

The narrative explores the dragon's attempts to clear his name and live peacefully, often through humorous and ironic situations. His interactions with humans and other mythical beings highlight the absurdity of the misconceptions surrounding him. The dragon’s calm demeanor and reluctance to engage in violence contrast sharply with the aggressive and often misguided actions of those who seek to challenge him. Over time, the dragon forms unexpected bonds with certain humans and creatures who come to understand his true nature, leading to moments of camaraderie and mutual respect.

Key characters include the dragon himself, whose patience and wisdom are central to the story, and a variety of human and mythical figures who either perpetuate or challenge the dragon's villainous reputation. The manga blends comedy, fantasy, and slice-of-life elements, using the dragon’s plight to explore themes of prejudice, misunderstanding, and the consequences of blindly following societal narratives. The story unfolds in a lighthearted yet thought-provoking manner, offering a unique twist on traditional dragon lore.