In 2015, the Chaldea Security Organization enlists scientists from both the magical and mundane sciences to monitor humanity's future for probable extinction events. Humanity's existence appears to be secured for the next century—until the judgement changes, and extinction of the species now awaits at the end of 2016. The reason is unknown, however it appears to be connected to the Japanese village of Fuyuki and events in 2004 during the Fifth Holy Grail War. Chaldea responds by utilizing an experimental method of time travel, the Rayshift technology. Ritsuka Fujimaru, a young man just enlisted to the organization, and the enigmatic female Mash Kyrielight can use it to travel back to 2004 and figure out how to preserve mankind. A tremendous command to combat fate has been issued.