In 2015, the Chaldea Security Organization recruits experts from both the magical and mundane fields to monitor humanity's future for potential extinction events. Human survival appears guaranteed for the coming century—until the prediction abruptly shifts, revealing that the species faces eradication by the end of 2016. The cause remains unknown, though it seems connected to the Japanese town of Fuyuki and the events of the Fifth Holy Grail War in 2004. In response, Chaldea utilizes an experimental time-travel method known as Rayshift technology. Using this system, Ritsuka Fujimaru, a young man recently recruited to the organization, and the enigmatic girl Mash Kyrielight, can journey back to 2004 to uncover how to save humanity. A grand order to defy fate has been issued—an order to alter the past and restore the future.