Humans and dragons once lived together peacefully on the continent of Elibe, but a thousand years ago, a fierce conflict erupted between humans and dragons, known as "The Scouring," which resulted in the dragons being driven out of the continent. Nearly a thousand years later, two great human kingdoms still maintain a balance of power on Elibe: Etruria in the west and Bern in the east. However, this balance is shattered when Zephiel, the king of Bern, begins invading neighboring countries with a powerful army bolstered by dragons that many thought to be extinct. The invasion of Bern proves unstoppable, and one by one, Bern's neighboring countries fall under Zephiel's control. To the south, the Lycian League raises an army to defend against Bern's invasion. Among this army is Roy, a young noble from Pherae, who has just stepped in to take his ailing father's place. The conflict continues, and Guinivere, Zephiel's younger sister, entrusts Roy with Bern's greatest treasure, the Fire Emblem. As Roy embarks on his journey, he grows ever closer to discovering the true meaning of "The Scouring."