Hope's Peak Academy is an elite high school that accepts only the most talented students. Individuals who successfully enroll receive their own unique titles, suitably reflective of their skills and traits. Of the fifteen candidates admitted to the peculiar school that year, Makoto Naegi is a completely ordinary individual who has been accepted by sheer chance, with the title of "Super High School-Level Luck." Naegi and his fellow classmates are initially ecstatic to be chosen to study at this prestigious institution, but these feelings of happiness are short-lived. They are soon confronted by Monokuma, the principal and resident bear, who traps them inside the school. The pupils' hopes of escape and graduation hinge on one of them successfully murdering one of their peers without being discovered. However, if the killer is caught, he or she will be executed, and the remaining survivors will be left to continue the deathmatch until only a single victor remains. [Written by MAL Rewrite]

Princess Anisphia "Anis" Wynn Palletia has always dreamed of flying through the sky, even though the people of her kingdom consider it a silly ambition. Also at odds with her goal is the fact that Anis is incapable of using magic despite her noble status. Refusing to give up so easily, she renounces her right to the throne, and focuses on developing "magicology" by combining various resources with knowledge from her previous life on Earth. Due to Anis' nature, responsibility for the kingdom's future is passed onto her younger brother, Algard. Pushed into a political marriage with Euphyllia Magenta, a girl he hardly knows, Algard rebels by spending more time with a commoner girl than his fiancée. After Euphyllia tries to intervene, Algard publicly calls off their marriage and denounces his ex-fiancée as a bully. After crashing into the banquet where Algard makes the announcement, Anis rescues Euphyllia on the flying broom she is testing. She decides to make Euphyllia her assistant, which the other girl reluctantly agrees to. Although their partnership appears random at first, Anis has an ulterior motive for wanting Euphyllia's company.

In 19th-century France, the wife of vampire noble Jean Duchet Godard is murdered in her own home. With the local human authorities unwilling to properly investigate the case, Godard hires a pair of private detectives known to specialize in the supernatural: Tsugaru Shinuchi, a man with a mysterious birdcage; and his partner, Aya Rindou. This enigmatic duo has come from faraway Japan for one purpose—to track down the man who stole both Aya's body and Tsugaru's humanity.

Daisuke Kanbe, a man of extraordinary wealth, is assigned to the Modern Crime Prevention Headquarters as a detective. It is there that he gets partnered with Haru Katou, a humane detective who values justice above all. The two are polar opposites, and their morals clash time and time again. Haru despises Daisuke for using monetary wealth to solve cases, as he believes that money isn't everything. The two will have to combine their efforts, however, to solve the mysteries that are coming their way. [Written by MAL Rewrite]