"My Hero Academia's" overarching plot revolves around the destined conflict between the wielders of two powerful Quirks: One For All, a power that stockpiles strength and can be passed down, and All For One, a power that allows its user to steal and redistribute Quirks. The series reveals that these Quirks were created by two brothers, with All For One being the villainous elder brother and the first user of One For All being his seemingly Quirkless younger brother who was forced to take a power-stockpiling Quirk.
A major twist reveals that Tomura Shigaraki, the leader of the League of Villains and All For One's successor, is Tenko Shimura, the grandson of Nana Shimura, who was the seventh user of One For All and All Might's mentor. This creates a deeply personal and tragic conflict, as All Might's legacy is destined to fight the legacy of his beloved master.
Key plot turns include All Might's forced retirement after his pyrrhic victory over All For One, which shatters society's sense of security. Another shocking reveal is that the villain Dabi is actually Toya Todoroki, the long-lost and presumed-dead eldest son of the hero Endeavor, who is using his public platform to expose his father's abuse and destroy public trust in heroes. Furthermore, it's discovered that the U.A. traitor is Yuga Aoyama, who was blackmailed by All For One.
Izuku Midoriya eventually learns that One For All contains the Quirks of all its previous users, and he begins to awaken these additional powers, such as Blackwhip. After the devastating Paranormal Liberation War, hero society collapses, and Izuku leaves U.A. High to protect his friends, operating as a lone vigilante in what is known as the "Dark Hero Arc." He is eventually brought back by his classmates, led by Bakugo who offers a heartfelt apology for his years of bullying, cementing their changed dynamic.
The manga's finale sees the final confrontation where Izuku, with the help of his friends, defeats a fused All For One/Shigaraki. In the final battle, Izuku is forced to transfer the embers of One For All into Shigaraki to defeat him from within, losing his powers in the process. In an epilogue set years later, a Quirkless Izuku becomes a teacher at U.A., but is gifted a powered suit by his friends, allowing him to continue his hero work.