At Chaldea Security Organization, the final Master of humanity Ritsuka Fujimaru and his Servant Mash Kyrielight have journeyed through six regions of differing eras in order to retrieve their future lost due to the "incineration of humanity" caused by the Mage King. And now, to repair the final Singularity, the pair head forth into ancient Mesopotamia. As soon as they land in those lands where the gods exist on an everyday basis, they are assaulted by an overwhelming number of Demonic Beasts. And just as suddenly, a beautiful girl descends down from the sky.

Due to overwork, Gilgamesh finds himself in the arms of eternal sleep. Fujimaru and the others are shocked by the news. They also hear from Siduri that there have been many reports of deaths from weakness within Uruk. Thinking that a member of the Three Goddess Alliance is the cause of it all, they head to the underworld with Ishtar to defeat the goddess of the land of the dead and liberate Gilgamesh’s soul.