In the bustling Naruhata district of Tokyo, a college student named Koichi Haimawari uses his Quirk, Slide and Glide, to perform small acts of kindness, such as returning lost items or helping people carry heavy loads. Though he dreams of being a hero, his power is modest and he lacks a license, limiting him to minor good deeds done in secret. His quiet life changes when he and an aspiring teenage idol and street performer named Kazuho Haneyama, also known as Pop Step, are attacked by thugs. They are saved by a mysterious and brutally efficient masked vigilante who calls himself Knuckleduster.

Knuckleduster, a man with no Quirk but immense physical strength and detective skills, sees potential in the pair and forcibly recruits them to become vigilantes. Operating outside the law, the unlikely trio forms the Naruhata Vigilantes, taking on crimes that are too small for professional heroes to notice and too large for ordinary citizens to handle. Their mission becomes urgent with the spread of a dangerous new drug called Trigger, which artificially amplifies a person's Quirk, turning ordinary civilians into rampaging, instantaneous villains. As they battle these enhanced criminals, they uncover a vast criminal syndicate known as the Villain Factory.

The heroes the group encounters are younger versions of familiar characters from the main My Hero Academia story. A young Shota Aizawa, who will one day become the hero Eraserhead, regularly clashes with the vigilantes while also begrudgingly acknowledging their effectiveness. He is joined by his U.A. High School classmates, including the loud Present Mic and the ill-fated Oboro Shirakumo. Other pro heroes such as Midnight, Ingenium, and the American hero Captain Celebrity also play significant roles as the vigilantes' actions increasingly intersect with official hero work.

As the story progresses, Koichi evolves from a timid Nice Guy into a confident fighter known as The Crawler, mastering his seemingly weak Quirk in creative ways. Kazuho grapples with her dual identity as a pop idol and a crime-fighter, while Knuckleduster pursues a personal vendetta against the Villain Factory, which is connected to the disappearance of his daughter. The narrative spans several major arcs, including an investigation in Osaka alongside the hero Fat Gum, a large-scale crisis at the Tokyo Sky Egg event, and a deep dive into Aizawa's tragic school days. The final arcs see the vigilantes face their greatest challenge against the villainous Number 6, leading to a city-wide lockdown and a final performance that decides the fate of Naruhata, all while setting the stage for the world of professional heroes seen in the main series.