If not for his ability to take over people's mind and body, Yuu Otosaka would be an ordinary high school student. Though it only lasts for five seconds at a time, Yuu's mysterious power allowed him to cheat his way to the top of his class and enter a prestigious high school, where he continues his dishonest acts. His shenanigans are eventually stopped by Nao Tomori—the headstrong student council president from Hoshinoumi Academy—who sees through his deceit. Through coercion, Nao convinces Yuu to transfer to Hoshinoumi and join the student council. Hoshinoumi Academy is secretly an institution created for adolescents who possess supernatural abilities—with the student council serving as a means of locating those who abuse their powers. With Yuu begrudgingly assisting in council affairs, the group sets out to find and protect new ability users from harm. However, as they further investigate the abilities, their findings entangle them in far more complicated matters than they could ever imagine.

Shigeo Mob Kageyama is now maturing and understanding his role as a supernatural psychic that has the power to drastically affect the livelihood of others. He and his mentor Reigen Arataka continue to deal with supernatural requests from clients, whether it be exorcizing evil spirits or tackling urban legends that haunt the citizens. While the workflow remains the same, Mob isn't just blindly following Reigen around anymore. With all his experiences as a ridiculously strong psychic, Mob's supernatural adventures now have more weight to them. Things take on a serious and darker tone as the dangers Mob and Reigen face are much more tangible and unsettling than ever before.

Asta and Yuno were abandoned at the same church on the same day. Raised together as children, they came to know of the Wizard King—a title given to the strongest mage in the kingdom—and promised that they would compete against each other for the position of the next Wizard King. However, as they grew up, the stark difference between them became evident. While Yuno is able to wield magic with amazing power and control, Asta cannot use magic at all and desperately tries to awaken his powers by training physically. When they reach the age of 15, Yuno is bestowed a spectacular Grimoire with a four-leaf clover, while Asta receives nothing. However, soon after, Yuno is attacked by a person named Lebuty, whose main purpose is to obtain Yuno's Grimoire. Asta tries to fight Lebuty, but he is outmatched. Though without hope and on the brink of defeat, he finds the strength to continue when he hears Yuno's voice. Unleashing his inner emotions in a rage, Asta receives a five-leaf clover Grimoire, a Black Clover giving him enough power to defeat Lebuty. A few days later, the two friends head out into the world, both seeking the same goal—to become the Wizard King!

After the murder of her father, Ryuuko Matoi has been wandering the land in search of his killer. Following her only lead—the missing half of his invention, the Scissor Blade—she arrives at the prestigious Honnouji Academy, a high school unlike any other. The academy is ruled by the imposing and cold-hearted student council president Satsuki Kiryuuin alongside her powerful underlings, the Elite Four. In the school's brutally competitive hierarchy, Satsuki bestows upon those at the top special clothes called Goku Uniforms, which grant the wearer unique superhuman abilities. Thoroughly beaten in a fight against one of the students in uniform, Ryuuko retreats to her razed home where she stumbles across Senketsu, a rare and sentient Kamui, or God Clothes. After coming into contact with Ryuuko's blood, Senketsu awakens, latching onto her and providing her with immense power. Now, armed with Senketsu and the Scissor Blade, Ryuuko makes a stand against the Elite Four, hoping to reach Satsuki and uncover the culprit behind her father's murder once and for all.