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.

Despite not understanding much about fleeting teen romance, first-year high school student Kazuhiko Nukumizu still wonders how he would react if his life were to be turned into a love story. Regardless, as a self-proclaimed background character, Nukumizu is satisfied continuing his life as an introvert with a negligible social life. However, he suddenly finds himself too close to the spotlight when he witnesses his popular classmate Anna Yanami be rejected by her childhood friend in the middle of a family restaurant. While Nukumizu wishes he could just forget what he saw and move on, Anna ends up forcefully confiding herself in Nukumizu, lamenting her status as a childhood friend fated to have her beloved stolen. As he becomes dragged into Anna's situation, Nukumizu soon gets caught up in the relationship drama of two more girls: Lemon Yakishio, an outgoing member of the track and field club; and Chika Komari, a shy member of the literature club. Now thrust out of his comfort zone, Nukumizu finds himself a major character in the lives of too many losing heroines.

Yuuta Hibiki wakes up in the room of Rikka Takarada and notices two things: he has no memories, and he can hear a mysterious voice calling his name from a nearby room. On further inspection, he finds a robot—which introduces itself as Hyper Agent Gridman—behind the screen of an old computer. Much to Yuuta's surprise, Rikka cannot hear Gridman, nor can she see the ominous monsters looming over a thick fog as it envelopes the town outside. Another giant monster materializes in the city and proceeds to wreak havoc. Amidst the confusion, Yuuta is once again drawn to the old computer and merges with Gridman. Suddenly, he appears in the middle of the battle and is forced to fight the monster. Together with Rikka and fellow classmate Shou Utsumi, Yuuta forms the Gridman Alliance to defeat the monsters plaguing the city and find whoever is responsible for their emergence.