The story begins with Yggdrasil, a popular online game which is quietly shut down one day; however, the protagonist 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) begining 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.

On the outskirts of Tokyo stands Hachimitsu Private Academy, a storied all-girls boarding school for elite young women full of potential and good breeding. But as the new school year rolls around, one tradition is going out the window: For the first time in the school's long history, boys are being allowed to enroll. But on the first day of school, only five boys make the cut. Kiyoshi Fujino, one of the lucky few, is thrilled by this discovery, his heart leaping with joy at the thought of being surrounded by all those girls, day in and day out. But little does he know of the shocking fate that awaits him.

When Hotaru moves into a new apartment alone, there's a mysterious man standing nearby the apartment. Hotaru decides to confront the man, who turns out to live in the neighboring apartment. The next day at school, Hotaru's best friend Kanae tells Hotaru that a host tricked her out of her money. When Hotaru goes to confront the host, he happens to be none other than Hotaru's neighbor, Masamune?!

Very few adolescent boys and girls have an onset of special abilities. Yuu Otosaka uses his ability unbeknownst to others in order to lead a satisfying school life. And then, a girl named Nao Tomori suddenly appears before him. Their encounter reveals the destiny for wielders of special abilities.

A gate appears in Tokyo's Ginza district sometime in the 21st century. From the gate pours out monsters, knights from middle-age Europe, and other fantasy-like beings, and they kill many of the citizens of Tokyo. This event is known as the Ginza Incident. The government sends a small group of soldiers from the Japanese Self-Defense Forces to the alternate world beyond the gate. Led by otaku soldier Yōji, they find that the villages in the world are being attacked by a dragon. An elf girl who is a survivor from the dragon's rampage joins the group in their travels across the dangerous new world.