The League of Villains is being pursued by Endeavor and Hawks, while driving off in a truck carrying mysterious cargo. After destroying the truck, despite failing to apprehend the League members, the heroes find an empty life support capsule. The man inside, Nine, a villain, has escaped and regroups with his team of villains, planning to create a society where those with strong Quirks rule over others.
U.A. High’s Class 1-A has been sent to the remote Nabu Island as part of a safety program. Izuku Midoriya, the holder of One for All, meets Mahoro Shimano, and her brother Katsuma, residents of the island. Bonding with them along with his rival Katsuki Bakugo, they discover that Katsuma wishes to become a hero, but Mahoro seeks to dissuade him, believing his Quirk to be unsuited for that line of work.
Meanwhile, Mahoro and Katsuma’s father is attacked by Nine and his party, with Nine stealing his Quirk. Nine, who has been empowered by All For One, can steal and possess up to nine Quirks, but his body cannot handle these Quirks without suffering damage. He seeks to use the stolen Quirk to heal himself, becoming near-invincible, but the stolen Quirk is incompatible with his blood type. Nine surmises that the man’s children might possess a better variant of it, and pursues them.
Nine and his gang arrive on the island and destroy all means of escape and communication. Class 1-A learns of the invasion and split up to stop the villains and protect the island residents. Nine finds the children and confirms Katsuma possesses the Quirk he seeks, but Midoriya intervenes before he can steal it; however, neither he nor Bakugo are a match against Nine. Despite this, they force him to retreat due to overusing his Quirks.
Class 1-A regroups and decide to attack the villains head-on, while awaiting the arrival of other heroes. Upon evacuating the islanders, the class manage to defeat the rest of Nine’s crew, but are incapacitated by Nine, except for Midoriya and Bakugo. Seeing no other way to defeat Nine, A desperate Midoriya transfers One For All into Bakugo, while he uses leftover embers of its power. Together, the two overpower and defeat Nine, but Midoriya’s One For All seemingly fades afterwards.
As professional heroes arrive, All Might finds an unconscious Bakugo and Midoriya. He realizes that One For All remains within Midoriya, as the transfer into Bakugo was interrupted, theorizing that the previous wielders of One For All wish for Midoriya to keep it. On a nearby island, Tomura Shigaraki finds and spitefully kills the weakened Nine, promising to create the world Nine wanted, with Shigaraki as king.
With Nine’s gang apprehended, the class repair damage to the island before returning home. Midoriya and Bakugo, who has lost his memory of wielding One For All, say goodbye to Katsuma and Mahoro. The movie ends as Midoriya assures Katsuma he can become a hero, as All Might had done for him previously.