In the year 2138, virtual reality gaming is booming. Yggdrasil, a popular online game is quietly shut down one day. However, one player named Momonga decides to not log out. Momonga is then transformed into the image of a skeleton as "the most powerful wizard." The world continues to change, with non-player characters (NPCs) beginning to feel emotion. Having no parents, friends, or place in society, this ordinary young man Momonga then strives to take over the new world the game has become.

In the Four Islands Archipelago, people can use Grav-Shoes to fly around! This is the story of Asuka Kurashina, a transfer student that arrives at Kunahama Academy from outside the Four Islands. After seeing the ability of wearers to soar in the sky, she quickly develops an interest in flying with the Grav-Shoes and also joins the school's FC (Flying Circus) club to further her passion.