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.

Fujimaru and Mash head for Uruk, led by a young man named Enkidu who has volunteered to be their guide. However, within the deep forest, Mash feels an ominous feeling in the air as Enkidu walks down a path different from the direction of their destination. Before them, an aloof couple – a man and a girl – appear before them. And with one phrase from the man, the hidden secrets of Enkidu come into light...

Fujimaru's entourage successfully has an audience with the wise king Gilgamesh ruling over Uruk. Fujimaru suggests to Gilgamesh that he wants to receive the Holy Grail that is causing this Singularity in return for defeating the Three Goddess Alliance that is putting all of Mesopotamia into a panic. However, Gilgamesh declares that he will not need the assistance of Chaldea for Uruk to face its perils. The situation turns extremely delicate, but then, Ishtar, the patron deity of Uruk, suddenly intrudes upon them, and they all end up in battle.

Fujimaru recalls his journeys in the other Singularities, particularly the regret he feels for those he couldn't save. Fujimaru finds himself questioning his decisions. Meanwhile, Gilgamesh dispatches him to investigate the city of Ur under royal orders.

Fujimaru and company are dumbfounded by Gilgamesh's sudden visitation of the Chaldean Embassy. There, they are given a new request from the king which is to investigate the Persian Gulf. Merlin and Ana cannot join as they have no travel permits. In other words, this will be Fujimaru's first journey alone with Mash in a while. But there sat the noble king, reciting a poem and cocking his head in contemplation. Having fun with tales of the past, Fujimaru and company's journey will finally become a lively one.

Finishing up the investigation at the Persian Gulf, Fujimaru and company are given a new order from the king. The new order is to retrieve a clay tablet that Gilgamesh had previously lost in the city of Kutha. Kutha was a city that suddenly disappeared after the emergence of the three goddesses, where every citizen had passed away. In such a quiet town, the entourage decides to split up in search of the tablet. Fujimaru suddenly wanders into a very frigid world. It is what people call "the underworld," a space separate from the physical world.

Fujimaru successfully retrieves Gilgamesh's clay tablet, and within a deep slumber, he remembers his encounter with the King of Mages in London, the Fourth Singularity, which renews his understanding of the importance of the final Holy Grail. Meanwhile, Merlin suspects that the Demonic Beasts at the Northern Wall are planning a large-scale attack, and takes Fujimaru and company to the Northern Wall. There, they see a squad commanded by Leonidas I putting up a struggle. Once there, Fujimaru and company hear from Ushiwakamaru that communication with the fortress city of Nippur to the north has been severed, and they head out towards Nippur.

Fujimaru and entourage, in order to rescue the people left behind in the fortress city of Nippur after communications were severed, begin their battle against the fake Enkidu who had been awaiting them. With Fou's help, they were somehow managing to keep things even, but in the midst of battle, the Goddess of the Demonic Beasts finally appears. Even Merlin is at his wit's end facing her overwhelming power. Meanwhile, Ushiwakamaru and Leonidas I engage in a spectacular battle, standing up defiant against the Goddess of the Demonic Beasts. In order to break through the situation where it is hard to deliver a wounding blow, the two Servants unleash their Noble Phantasms with desperate resolve.

Fujimaru and entourage have lost Ushiwakamaru and Leonidas I. Upon receiving the report from the group that returned to the ziggurat, Gilgamesh decides it is necessary to conquer the three goddesses in certain order to fight against Gorgon, and orders Fujimaru to first turn Ishtar into an ally. With a "secret plan" given by Gilgamesh in hand, Fujimaru and company head over to Ishtar's temple.

Fujimaru and company greet Ishtar to their ranks without hitches, and gain information from Gilgamesh about the key for defeating Gorgon, "the Axe of Marduk" stowed away in Eridu within the southern jungle.

Fujimaru and company ever so easily have Jaguar Warrior join their ranks, and are reunited with the soldiers of Uruk, thought to be all dead, outside Eridu.

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.

Fujimaru confronts Ereshkigal, the goddess of the underworld, and pleads with her to join with him to help save Uruk. Incensed, Ereshkigal refuses and attacks Fujimaru and his companions. With help from Gilgamesh and Ishtar, Fujimaru again attempts to persuade Ereshkigal, however... the goddess instead opts to fulfill her appointed duties.

After making peace with Ereshkigal, goddess of the underworld, Fujimaru and the others return to Uruk to find Gilgamesh, who has returned to the land of the living. As the final battle with Gorgon approaches, Gilgamesh proposes a strategy that may give them a chance at victory.

With the Axe of Marduk, Fujimaru’s party manages to weaken Gorgon by lowering her Divinity. Having opened a path for themselves, they finally reach the Blood Fort’s depths. There, Gorgon says that she will gain her revenge by destroying humanity. Ana unleashes her own divinity, which had been suppressed until now, against Gorgon

The Laḫmu attack Kingu and steal the Holy Grail from his body! After being robbed of the Grail, Kingu makes a desperate escape into the forest. However, the Laḫmu discover him there, and so he prepares to meet his fate. But at that moment, Kingu witnesses something beyond comprehension... At the same time, Fujimaru and company pursue the Laḫmu now in possession of the Grail, but a Servant long thought dead appears to block their path.

The power of the Grail, now in the hands of the Laḫmu, has transformed the Persian Gulf into the Chaos Tide. Any living thing that touches this sea is instantly mutated into a Demonic Beast. As the Chaos Tide advances toward Uruk, Fujimaru and company form a desperate plan to destroy Tiamat as a last-ditch effort to save the city.

When Tiamat refuses to be defeated even after Quetzalcoatl’s desperate attack, Gorgon makes her appearance. The newcomer unleashes her devastating Noble Phantasm to destroy Tiamat’s wings but is unable to halt her advance toward Uruk.

Fujimaru and company finally succeed in defeating Beast II, though this victory was won with many sacrifices. The entire group is wounded and battle-weary, and as they take stock of the aftermath, they see that Uruk itself is on the verge of collapse. What will the end of their journey bring them?

Fujimaru, Mash and the goddesses enjoy one last moment of peace on the eve of the final battle. That same night, Kingu reaches the peak of the ziggurat. So badly injured that he can no longer stand, he looks up to see a figure looming over him... As morning dawns, King Gilgamesh gives Fujimaru and his companions some final words of encouragement. Their attack on Tiamat begins now!

Tiamat falls into the underworld, but there, she transforms into one of the Evils of Humanity: Beast II. Hassan-i Sabbah, the first Old Man of the Mountain, intervenes, using his power as Grand Assassin to deprive Beast II of her immortality.