The AmuSphere is nothing like the Nerve Gear. With safeguards in place to protect the users bodies, everyone thinks that there's no danger. However, after a pair of players playing a new Horror VRMMO based on the works of HP Lovecraft go berserk and kill their guild-mates IRL, it soon becomes clear that it's now the players minds that are on the line.

After Asuna, Kirito, and Kizmel depart the fifth floor of Aincrad for the final time, they leave behind Yofel Castle, and the burgeoning AI of one Viscount Leyshren Zed Yofilis. Left with an odd feeling of emptiness after the departure of the trio, Leyshren sets out on his own journey to discover why both he, and the world he lives in, seem to be changing so drastically.

Five years have passed since the events of the IS Anime. Charlotte and Laura have become teachers at the IS Academy while Ichika and company are taking part in the World IS Championships. Yet darkness stirs beneath the surface: A mysterious man connected to Chifuyu's past arrives at the Academy with a dire warning, and everything is not as it seems at the Championships either.