Lured by new technology from Rath, Kirito must once again dive into the Underworld to find Eugeo's soul, in the hopes that he can bring his best friend back. Once inside the Underworld, Kirito discovers people have gone missing and there is a plot to resurrect the Pontifex. However, new technology always comes with a price and sacrifices must be made.

After learning of Kirito's betrayal to stay and protect Alice and the Underworld, Eugeo falls victim to Administrator's will once again. After gaining knowledge found on a laptop in the Central Cathedral, the Pontifex decides to 'upgrade' Eugeo to match the level of the swordsman who killed her. Now, things are personal and revenge will be sweet.