As part of the Hero Work Recommendation Project program sponsored by the Hero Public Safety Commission, Class 1-A are stationed as a Hero Agency on the isolated and peaceful Nabu Island. This training exercise is intended to help them become the next generation of heroes; as the island never sees extreme villain crime, the students can help out around the town without the direct supervision of their teachers.
One night, two siblings, Mahoro and Katsuma Shimano, warn Izuku and Katsuki about a villain attack, but they realize that everything is an illusion created by Mahoro with her Hologram Quirk. Katsuki angrily scolds both for having faked a villain attack before Izuku restrains him while the two kids run away. The next day, Izuku comes across Katsuma again, who apologizes for his sister's prank last night. After Katsuma leaves, a neighbor informs Deku he kid's mother died and the village watches after them while their father is away working.
The peace of the island is interrupted when it is invaded by Nine and his gang. Nine is a villain who dreams of creating a world where the strong rule over the weak. He is the possessor of a powerful Quirk that allows him to manipulate the weather, however it also causes the destruction of his cells. Looking for a cure, Nine underwent an operation by Kyudai Garaki, who implanted in his body a less powerful version of the All For One, allowing Nine to steal up to eight Quirks. With this power, Nine stole the Quirks from various heroes and looked for any Quirk that could cure him of his illness.
Somehow he discovered that the father of Katsuma and Mahoro is the holder of a Quirk known as "Cell Activation", which could stop the degeneration of his cells, so he attacked him and stole his Quirk. However, the quirk did not work because it was incompatible with his blood type. Without losing hope, Nine decided to look for Mr. Shimano’s children, hoping that at least one of them had inherited the Quirk.
After hijacking a ferry and crashed into the harbor, Nine orders his teammates to isolate the island from the outside and cause much destruction as possible in order to divert attention from their true goal. While Slice, Chimera, and Mummy attack the town and its citizens, Nine hunts down the siblings. When they see the villains destroying the port, Mahoro calls the agency to tell Katsuki about the villain attack. He doesn't believe her at first but Izuku hears the exchange and runs off to help. Izuku immediately goes out to help the children, and the rest of the classmates soon realize the situation and organize to face the villains.
Meanwhile, Mahoro and Katsuma run away from the scene of the fighting and attempts to get back home but it’s destroyed by Nine himself. The villain uses his Quirk to scan the little kids and found out that Katsuma has the Cell Activation Quirk and the exact blood type he needed. Mahoro uses her Hologram Quirk to create a monster that attacks the villain, but it does not work because Nine knows that it is only an illusion. Before Nine can steal Katsuma's Quirk, Izuku arrives in time and rescues the kids, using his Quirk to escape through a forest area and get the kids to safety. Izuku tells them to run away while he faces Nine in the forest area.
Izuku demands to know why he is chasing the children but Nine just orders him to back off, warning him that he will kill him if he gets in his way. Izuku activates his One For All: Full Cowl - Shoot Style at 8% and attacks with a flying kick. Nine uses his Air Wall to shield himself, forcing Izuku to back off
He thinks that barrier quirk is Nine's only power when suddenly the villain starts shooting him with purple Bullet Laser emerging from his fingers. Using the trees of the forest, Izuku manages to dodge the beams, surprised that Nine has another Quirk in addition to his Air Wall. This makes Izuku think that Nine is almost like All For One.
Izuku uses his Delaware Smash Air Force to shoot projectiles of compressed air against Nine, who defends himself with his Air Wall. Nine comments the interesting way that Izuku uses his Quirk before using another quirk that launches a gust of wind, making Izuku momentarily lose his balance. Nine tries to take advantage and shoots more purple beams at him. Deku manages to dodge the attacks, being slightly wounded in the cheek.
Not knowing how many Quirks his enemy can have, Izuku considers that his best option is to strike first, so he activates One For All: Full Cowl at 20% and attacks with a St. Louis Smash. Thanks to his Scanning Quirk, Nine perceives Izuku's remarkable increase in strength, thus creating an even more powerful Air Wall to counter Deku's attack.
Using his Scanning Quirk, Nine thinks that it is worth snatching and keeping the Izuku’s Quirk, so he restrains Deku despite his abilities and uses his All For One Quirk to steal One For All. However, something stopped the process, leaving Izuku temporarily immobile. Nine is surprised that he can't steal Izuku's Quirk and assumes it is because it doesn't fit in the slot. Nine is impressed that Izuku is the holder of a Quirk with so much potential, but since he is unable to take it away, Nine decides that it is best to delete it, so he uses his Air Wall Quirk at a defenseless Izuku, slamming him hard against a nearby hill.
While trying to recover from the impact, Izuku realizes that neither Mahoro nor Katsuma had moved away from the place. The children try to help him, but Izuku orders them to flee. Before he could get up, Nine proceeds to shoot a purple laser at Izuku's chest, wounding him. Frightened, Mahoro uses her Hologram Quirk to project a cartoony version of the wounded Izuku as a distress beacon to alert everyone on the island about their whereabouts.
Katsuki, who had already defeated one of Nine's subordinates, arrives and engages combat with Nine. He blasts him with an explosion but the villain managed to protect himself with his barrier in time. After boasting to Izuku and the children that he will be the number 1 hero, Katsuki charges Nine, who uses his Air Wall again. Using his mobility, Katsuki positions himself above him and prepares to shoot another explosion, but Nine is faster and attacks him with his Bullet Laser Quirk. Katsuki dodges beams in midair, but Nine knocks him down with an air blast.
Katsuki recovers, and Izuku warns him that Nine owns several Quirks and is also capable of stealing them, similar to All For One. Katsuki attacks again and is able to adapt to Nine's different Quirks. He manages to outsmart the villain and gets behind him, but when he is about to burst him, Nine summons a large blue snake-shaped attack from his back that catches Katsuki with his jaws and crushes him to the ground.
Izuku manages to recover, and despite the blow and still being caught in the jaws of the Hydra attack, Katsuki uses his Explosion Quirk to block Nine's vision and give Izuku a chance to strike. Nine uses his Scanning to detect Izuku, being close enough to land a blow at him. Nine realizes the danger posed by that attack, and instinctively uses his original Weather Manipulation Quirk to summon a massive lightning strike to zap Izuku and Katsuki, severely injuring them in the process, while at the same time, causing a major blackout throughout Nabu Island.
Considering that he has defeated his adversaries, Nine focuses his attention on Mahoro and Katsuma, who hug in terror. He barely takes a step when the almost unconscious Izuku and Katsuki grab the villain by the legs, willing not to allow Nine to harm the children. Nine uses his Air Wall to deliver the coup de grace to both students.
With Izuku and Katsuki down, Nine goes after the children when suddenly he begins to feel excruciating pain, His cells start to degenerate from overusing his Quirks during the fight. Barely conscious, Izuku witnesses this. Slice arrives to help his leader and Nine orders her to take Katsuma, but Koji Koda uses his Anivoice Quirk to summon a swarm of crows to blind the villains while Mezo Shoji, Tsuyu Asui, and Ochaco Uraraka rescue the wounded Izuku and Katsuki and the children.
Nine orders Slide to chase them but she assures him that they cannot leave the island and what they must do now is withdraw so that he can recover. With the kids gone and Nine in pain from his cell degeneration disease and is unable to continue fighting. Slice arrives to take Nine away and fires a flare gun to signal her fellow villains to retreat.
Night comes, and Class 1-A students regroup and shelters everyone in a factory to treat the wounded and provide humanitarian aid to the local residents. Izuku and Katsuki are both unconscious and the medical staff from the hospital clinic are able to close their wounds, but they cannot treat them any further because they've suffered so much damage that they need to be sent to a hospital in the mainland. Fortunately, Katsuma arrives and uses his Cell Activation quirk to heal both Izuku and Katsuki, allowing for quicker recovery.
Later, Class 1-A holds a meeting to discuss their plan going forward. Momo created a drone to send an SOS out to the mainland but won't arrive for six more hours. They try to figure out what the villains are after and Katsuma reveals Nine is trying to steal his Quirk. Izuku and Katsuki, having fully thanks to Katsuma, arrive in the meeting and encourages everyone to fight the villains and protect everyone on the island. The class, unanimously, agrees to fight the villains and Izuku devises a plan to defeat Nine and his henchmen.
Meanwhile, the villains regroup in a lighthouse. Chimera and Slice take care of their boss as he recovers from his illness, and are surprised to find that their teammate Mummy had been defeated and captured by the students. Despite these setbacks, the villains remain willing to carry on with their plans, preparing to launch a new assault the next morning.