Through their tutor Fuutarou Uesugi's diligent guidance, the Nakano quintuplets' academic performance shows signs of improvement, even if their path to graduation is still rocky. However, as they continue to cause various situations that delay any actual tutoring, Fuutarou becomes increasingly involved with their personal lives, further complicating their relationship with each other. On another note, Fuutarou slowly begins to realize the existence of a possible connection between him and the past he believes to have shared with one of the five girls. With everyone's feelings beginning to develop and overlap, will they be able to keep their bond strictly to that of a teacher and his students—or will it mature into something else entirely?

It is business as usual in the massive city of Orario, where legions of adventurers gather to explore the monster-infested Dungeon. Among them is the easily flustered yet brave Bell Cranel, the sole member of the Hestia Familia. With the help of his demi-human supporter Liliruca Arde and competent blacksmith Welf Crozzo, Bell has earned the title of Little Rookie by becoming Orario's fastest-growing adventurer thanks to his endeavors within the deeper levels of the Dungeon. Dungeon ni Deai wo Motomeru no wa Machigatteiru Darou ka II continues Bell's adventures as he tries to bring glory to his goddess and protect those he cares about. However, various familias and gods across the city begin to take notice of his achievements and attempt to add him to their ranks.

As Yumeko Jabami's fame grows and the reputation of the student council dwindles, Kirari Momobami decides to revolutionize the group. To this end, she announces an election for its next president. The rules are simple: each student in the school receives one chip. Whoever has the most chips by the end of thirty days becomes both the new president and the head of the Momobami clan. Upon receiving news of this development, the Momobami branch families spring into action. Eleven transfer students arrive at Hyakkao Private Academy, each aiming to lead both the school and the Momobami clan. Equipped with unique talents, they will compete to get as many chips as possible—but their chips are not the only things on the line.

One day, the bright red sun stopped shining, causing the Breakdown Phenomenon—the destruction of Arata Kasuga's town and the disappearance of the people inhabiting it. All, however, is not yet lost; by utilizing the magical grimoire given to him by his childhood friend and cousin Hijiri Kasuga, Arata's world gets artificially reconstructed. In order to investigate the phenomenon, Lilith Asami appears before Arata, whose artificial world suddenly disintegrates. He is given two choices: hand over the book, or die. However, Arata chooses the third option—enrolling in the top-secret magic school Royal Biblia Academy, where six other magical users await him. Together with Lilith, these six form the Trinity Seven, the elite of the school who each bolster their own power and skill. With the ambition to save Hijiri and the help of his newfound friends, Arata stops at nothing to prevent the destruction of his beloved hometown and to bring his best friend back.