Midgar Academy is a unique institution that stands out due to its acceptance of male students, specifically Yuu Mononobe, who was their first and only male student. However, what sets Midgar apart from other schools is its focus on training girls known as Ds, who possess extraordinary abilities in generating dark matter and manipulating it into powerful weapons. These Ds emerged after the mysterious appearance of destructive monsters called Dragons around the world. Despite their sudden disappearance, some girls were born with symbols on their bodies and powers similar to those wielded by the Dragons themselves. Today, these girls attend Midgar Academy in hopes of utilizing their abilities against the remaining Dragons. As the only known male D, Yuu must navigate relationships with his fellow students, including his long-lost sister who also attends the school, and work together to investigate and eliminate the threat posed by the powerful Dragons.
Juuou Mujin no Fafnir adapts the first 3 novels of Tsukasas light novel series of the same title.