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.

After failing his college entrance exams, 18 year-old Tsukasa Mizugaki is offered a position at the renowned SAI Corporation, known for its production and management of Giftia, androids that possess human emotions. Tsukasa’s position is in the terminal service department where the main job is to recover Giftias that are close to their expiration, a graveyard department in every sense. To make matters worse, Tsukasa is ordered to work with Isla, a female Giftia who is never given any responsibility other than serving tea to co-workers.

In the near future, spirits and monsters are in full sight. A boy leads a group of people with special abilities as they plot against a massive organization that takes advantage of a certain incident and eventually know the truth about their world in the process.