A young apprentice named Peru, studying under the legendary mask craftsman Gaston Roux, loses control after being possessed by a powerful artifact known as the Mask of the Warrior God. In a frenzied state, he unintentionally kills his fellow disciples and his master. Consumed by guilt and regret, Peru vows to prevent such a tragedy from ever happening again. He sets out on a solitary journey across the world to locate and destroy every last one of his master's creations, confronting the sins of his past while facing powerful enemies who seek to use the masks for their own ends.

The world of The Vermilion Mask is one where specially crafted masks grant incredible abilities to those who wear them, from the power of the Flame Dragon to the traits of a spider. However, these masks often demand a heavy price, and some possess a will of their own, leading to catastrophe when misused. As Peru travels, he is joined by companions who have their own connections to the masks. Sonarue is a former princess of Lisbran who, despite witnessing her mother's murder, retains her inner strength and chooses to leave her homeland to aid Peru. Mok is a young man unable to remove his smoke mask; while it grants him mastery over smoke, it forces him to smoke regularly to survive, and he joins the quest in hopes of one day taking it off.

The narrative follows Peru as he grapples with the weight of his actions, with the story emphasizing that his quest is not a noble atonement so much as a desperate necessity. Key arcs include his initial fall and the destruction of his master's workshop, the formation of his party as he encounters Sonarue and Mok, and a series of battles against other mask bearers, including those who covet the masks' power and others who have also been corrupted by them. The series builds toward Peru's ultimate confrontation with both the legacy of his master and his own desire for redemption, as the fate of his soul and the world hang in the balance.