A.D. 2016, the foundations of humanity have been incinerated by the Mage King Solomon. Chaldea, a secret mages organization with the mission to preserve humanity's future, foresaw mankind's extinction in 2015. Thus commenced the operation to repair the Singularities in history caused by Holy Grails dispersed across time and space—Operation Grand Order. Using the Rayshift time travel technology, Chaldea's last master Ritsuka Fujimaru and his demi-servant Mash Kyrielight have traveled to and resolved six Singularities. Now, they depart for their most dangerous destination yet: a civilization in the Age of Gods, B.C. 2655 Mesopotamia. Ritsuka and Mash soon discover that Demonic Beasts roam the land, attacking people and towns. Amidst chaos and terror lies humanity's last defense—Uruk, a fortress city that acts as the frontline for the battle against the beasts. The battlefront is commanded by none other than King Gilgamesh, the King of Heroes, who sought aid from Heroic Spirits and took on the role of a mage to protect his city. Along with Gilgamesh and the summoned servants, Ritsuka and Mash must protect Uruk against the magical beasts' onslaught and defeat the Three Goddess Alliance who aims to eradicate humankind; all the while, a greater threat looms over Uruk, preparing for its awakening.

Kimito Kagurazaka is a commoner with a fetish for men's muscles—or at least that's the lie he must keep telling if he wants to keep himself out of trouble at the elite all-girls school, Seikain Academy. Kidnapped by the school under the assumption that he prefers men, Kimito is made to be their commoner sample, exposing the girls to both commoner and man so that the transition to the world after school is not jarring. Threatened with castration should his sexual preferences not match the school's assumptions, Kimito keeps up the facade to protect his manhood. But there are eccentric individuals around every corner who begin to make Kimito's life even more difficult. Among them are Aika Tenkuubashi, a social outcast who blurts out whatever comes to mind; Hakua Shiodome, a young genius; Karen Jinryou, the daughter of samurai who is obsessed with defeating Kimito; and Reiko Arisugawa, the perfect student who has delusions of marrying Kimito. Along with the commoner himself, these four girls make up the Commoner Club, which attempts to teach the girls more about life outside the school, while Kimito gradually learns about the odd girls surrounding him.

Together with his talented aides, the Realist Hero Kazuya Souma continues his quest of reinvigorating the Elfrieden Kingdom through administrative reform. Having successfully conquered Van—the capital city of the Principality of Amidonia—Kazuya now faces the envoy from Gran Chaos Empire, who wishes to impose punishment for breaching the ban on war established by the Mankind Declaration Treaty. Despite the dire situation, Kazuya sees a path to avoid unnecessary conflict whilst gaining new allies. With his plan being seemingly perfect, the only barrier to success is gaining approval from the envoy.

The continent of Atlatan once again finds itself devoured by the flames of war after a horrific event known as the Great Hall Tragedy. What was supposed to be a joyful occasion that would establish peace between the Fantasia Union and the Factory Alliance, the marriage of Sir Alexis Douse and Lady Marrine Kreische, was instead a tragedy. As the bride and groom walked down the aisle, the ceremony was suddenly interrupted by a powerful convergence of Chaos, a dark energy from another dimension that corrupts the land and brings forth monsters and demons into the world. From within that energy appeared the Demon Lord of Diabolos, an evil being who instantly murdered the archdukes of both factions, shattering any hope for peace between them. Having failed to prevent this disaster, Siluca Meletes, an Alliance mage, is traveling through the Chaos-infested countryside to study under a master magician. When she is intercepted by a group of soldiers working with the Federation, Siluca is rescued by Theo Cornaro, a young warrior carrying a mysterious Crest, a magical symbol that gives its wielder the ability to banish Chaos. Bearing no allegiance to a specific domain, Theo hopes to attain the rank of Lord so that he can liberate his home town of Sistina from its tyrannical ruler and the Chaos spreading within it. Impressed by his noble goal, Siluca enters into a magical contract with Theo, and the two embark on a journey to restore balance to their war-torn land.