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—monitors the world as part of its mission to prevent the destruction of humanity.

It works tirelessly to ensure humanity's continued existence. Through the use of the Near-Future Observation Lens: Sheba, Chaldea finds proof that humanity will be destroyed in a cataclysmic inferno in the year 2019. Before long, a number of unobservable points in history suddenly appear throughout the timeline—they are referred to as Singularities.

Hypothesizing these events are what bring about humanity's extinction, Chaldea launches an operation to travel into the past. Ritsuka Fujimaru, Mash Kyrielight, Leonardo da Vinci, Romani Archaman, and other members of Chaldea embark on the Grand Order, a forbidden ritual in which they are able to intervene in the events of each Singularity in order to either resolve or eradicate them.

Now, a Seventh Singularity has been newly discovered in ancient Mesopotamia in the year 2655 B.C. During this time, Gilgamesh reigned over an age of prosperity as a wise king after the conclusion of his quest for the Herb of Immortality.

However, Mesopotamia is now on the verge of ruin at the hands of the Three Goddess Alliance and their hordes of Demonic Beasts.

After dismantling the city of Babylon in order to build the Fortress City of Babylonia, Wise King Gilgamesh continues to repel the attacks of these monstrosities. When Ritsuka Fujimaru and the others arrive at their Rayshift destination, they are attacked by a group of Demonic Beasts until a Servant named Enkidu comes to their aid. Before long, they come face-to-face with the legendary mage known as Merlin.

Gods... Demonic Beasts... Mankind... The battle to determine which will survive begins now.