In My Hero Academia: World Heroes’ Mission, a mysterious terrorist group called the Humanize are introduced. They strongly believe in the "Quirk Singularity Doomsday Theory." The theory states that as future generations continue to be mixed with the Quirk genes, the power it holds will lead to humanity’s demise. Furthermore, Humanize believes that Quirks are a disease, and so, they plan to “cleanse the world” by exterminating anyone who has one. Humanize planted "Ideo Trigger Bombs" in various countries, and these explosives are said to make a Quirk-user lose control of their Quirk, leading to mass destruction. To save and protect everyone, Pro-Heroes from around the world, and the U.A. Academy heroes-in-training, unite to thwart the efforts of the mysterious group.

Amakawa Haruto is a young man who died before reuniting with his childhood friend who disappeared five years ago. Rio is a boy living in the slums who wants revenge for his mother who was murdered in front of him when he was five years old. Earth and another world. Two people with completely different backgrounds and values. For some reason, the memories and personality of Haruto who should've died is resurrected in Rio's body. As the two are confused over their memories and personalities fusing together, Rio decides to live in this new world. Along with Haruto's memories, Rio awakens an unknown "special power," and it seems that if he uses it well, he can live a better life. But before that, Rio encounters a kidnapping that turns out to be of a princess of the Bertram Kingdom that he lives in. After saving the princess, Rio is given a scholarship at the Royal Academy, a school for the rich and powerful. Being a poor orphan in a school of nobles turns out to be an extremely detestable place to be.

During a blizzard, Masayuki Muroi's old high school friend pushes him off a mountain to certain death. However, Masayuki survives the fall and escapes to safety thanks to Yuki-Onna, the spirit of a beautiful young woman who is said to lead men to their demise—but all she asks in return is money. Eleven years later, Masayuki has lived a successful life, having gotten married and amassing a great fortune. But when his company collapses and his wife cheats on him, Masayuki retreats to the city where Yuki-Onna once saved him, and he reconnects with her by offering her money and tasty meals. While Masayuki recovers from his misfortunes, another one knocks on his door: his ex-wife is found beaten to death, and now only Yuki-Onna—who cannot reveal herself—can corroborate his alibi. With no one to turn to, Yuki-Onna enlists the help of the spirits' God of Wisdom, Kotoko Iwanaga. Revered by the various spirits that wander the earth, Kotoko uses her extraordinary wits and cunning to solve all quarrels they may have. In her duty to protect spirits and humans from colliding, Kotoko drags along her immortal boyfriend, Kurou Sakuragawa, and promises to prove Masayuki's innocence without exposing Yuki-Onna's existence.

The story tells the tale of Semi, a bright girl who goes in a magical time journey with the genius teacher Wai, in order to prevent the evil X from utilizing the powers of the magic cube for evil. Along the way, Semi and her math school friends run into history and math problems that they must solve with logic and wit.