Tasked with preventing the destruction of humanity, the Chaldea Security Organization—with its ability to see what cannot be seen with magecraft alone and to measure that which cannot be observed by ordinary science—continuously seeks out ways to ensure humanity's continued existence.

One day, Chaldea's worst fears are realized when the future it was observing suddenly vanishes. According to various calculations, humanity's eradication is certain in the year 2019.

At the same time, a number of unobservable points across history suddenly appear. Hypothesizing these are the cause of humanity's imminent extinction, Chaldea authorizes the Grand Order, an investigation with the purpose of either resolving or, if necessary, eradicating these events known as Singularities from the timeline.

Ritsuka Fujimaru and Mash Kyrielight are dispatched on a mission to the Singularity discovered in 1273 where unusual events are occurring in the Holy Land. Whereas this area should have been reclaimed by the Crusaders, the Singularity is slowly being rewritten into a history that should not be. On one side are figures from Camelot, including the Lion King and the Knights of the Round Table, and on the other, the ancient Egyptian Sun King, Ozymandias, has claimed a new kingdom of his own.

Can the damages done to this era by these two opposing powers be undone in order to prevent mankind's eventual extinction?