After deducing that the villain Nine is after Katsuma's Cell Activation Quirk, all Class 1-A members vow that they will protect him, his sister Mahoro and all the inhabitants of Nabu Island until reinforcements from the mainland arrive.
Izuku devises a strategy against Nine and his allies. His plan is to lure them to Mount Shiroyama, located on a small island near Nabu, and once there the students will attack the gang of villains to split them, so each of its members had to face several students alone. After his previous fight against Nine, Izuku concludes that Nine cannot use his multiple Quirks for too long as he suffers from intense pain when he does. To deal with Nine, everyone attacks him in waves to force Nine to use his Quirks all the time until he reaches his limit and cannot continue fighting.
The next morning, when the students see the villains approaching their position, they put their plan into practice. Yuga and Momo start attacking them from afar with their respective Quirks at full power, managing to separate Nine from his allies. Then the students take turns attacking him as they had planned. Despite their attempts to stop him, Nine gradually defeats the students, until it’s Izuku and Katsuki's turn to face him. After a tough fight, they finally get Nine to his limit and the backlash of overusing his quirk kicks in.
In his despair, the villain takes a heavy dose of a quirk empowering drug and goes beyond his limit, using his Weather Manipulation Quirk to summon a massive lightning, striking Izuku and Katsuki. The rest of the students try to apprehend Nine, but the villain easily defeats them and catches Katsuma and Mahoro up. He holds Mahoro hostage and threatens to kill her if Katsuma doesn't surrender his quirk. Katsuma runs towards Nine to save her but Nine tosses Mahoro to the side and tries to steal Katsuma’s Quirk. Before he can do it, Izuku and Katsuki enter the fray to save the children.
Izuku kicks Nine's face, and the force of the blow throws the villain several meters away from Katsuma. Then he apologizes to the little boy for the delay and praises him for his bravery. Meanwhile, Katsuki grabs Mahoro before she falls the ground and puts her down. Mahoro is glad to see him alive, and Katsuki replies that he had told her that he will be the number 1 hero. As the kids flee to safety, Deku and Katsuki proceed to fight Nine.
Izuku and Katsuki attack Nine in unison and he uses his Air Wall quirk to protect himself. The villain is understandably surprised that they survived his previous attack, and they explain that they had foreseen that he would reuse his trick for their first fight so they had Denki act as a lightning rod.
Izuku and Katsuki continue to press and manage to break through the barrier and take down Nine. The villain counterattacks by firing his Bullet Lasers but Katsuki counters his attack and bombards him. Nine then uses his Hydra attack, but Izuku tears them apart, giving Katsuki the chance to blast him. Looks like they are getting the upper hand as Nine is reaching his limits of using his multiple Quirks.
On the verge of defeat, Nine uses the remains of the quirk empowering drug in his life-support system to boost his Quirks to an even higher level, making himself superpowered. With his Weather Quirk amplified to the maximum, he generates a massive fire tornado while unleashing a violent lightning storm on the island, which he begins to destroy.
Knowing that Mahoro and Katsuma are still there and thinking about the innocent people taking refuge underground, Izuku boosts his Quirk to reach One For All: Full Cowl - 100% and uses Detroit Smash while Katsuki uses Howitzer Impact against Nine. They hold their attacks as long as they can, but their attacks are rendered useless against Nine’s tornado and get obliterated by it. Mezo manages to regain consciousness and uses his body to shield Katsuma and Mahoro from falling debris as the firestorm causes a cave-in, trapping Koda, Rikido, and Toru along with the civilians in the cave.
Izuku and Katsuki managed to survive, but they are severely wounded. The empowered Nine monologues about wanting to create a perfect society for those with powerful quirks live after erasing the weak. Deku and Katsuki look at him in disbelief, only to be decimated by his purple lasers. Then Nine uses his Hydra move and captures both Deku and Bakugou in its grasp. Nine continues talking about his utopia, which both Izuku and Katsuki consider selfish and stupid, so the villain starts crushing them to death.
All hope looks like it's lost. The entire class is down and wounded, and neither Izuku nor Katsuki are able to break free. But then they hear Mahoro and Katsuma cry out to them, asking them not to give up. Hearing their cries, Izuku makes a desperate decision.
He tells Katsuki that in order to continue this fight, there's only one thing they can do. Without further words, Katsuki understands what Izuku's plan is. Recalling the words of All Might, Izuku reaches his bloody finger out to Katsuki, and Katsuki extends his finger as well. They make contact and grasp hands firmly, transferring One For All to Katsuki.
Both break the grip from Nine, shocked at their new power. With Katsuki having One For All, he asks Izuku if he is even still capable of fighting, and Deku explains he is still was able to use One For All as he is holding onto the flickering embers of the quirk. Katsuki tells him that his decision will end his dream and Deku replies it's the only way, and that All Might would have accepted him as the next bearer.
Infuriated, Nine attempts to kill them by summoning another massive storm on the island, destroying much of the island's infrastructure. Izuku and Katsuki then power themselves up using One For All, reaching the 100%, and use Detroit Smash to stop the chaotic weather, punching into the sky and clearing away the powerful storm to blue skies.
Nine finds it hard to believe what just happened, yet he refuses to give up on fulfilling his dreams, and attacks Izuku and Katsuki with all his quirks at their maximum power. Despite his attempts, Izuku and Katsuki dodge and neutralize all his attacks. After a lengthy fight, Izuku and Katsuki finally manage to reach Nine. Katsuki prepares his final explosion and Deku prepares a finishing kick to Nine. Unleashing their powerful attack, they defeat Nine once and for all.
Both heroes pass out. As Izuku loses consciousness, he says goodbye to the last embers of the One For All, thanking it for everything.
After Class-1-A emerged victorious over the threat, the military and a large number of heroes arrive on Nabu Island, rescuing the civilians, medically treating Class 1-A, and putting the villains into custody.
All Might recovers the barely conscious Izuku and the unconscious Katsuki. He cradles Deku in his arms and says he did well, as Izuku asks if Bakugou is okay. Deku then starts crying as he apologizes to All Might for giving One For All to Katsuki because he had no other choice to protect the people on the island, before losing consciousness.
All Might forgives Izuku, saying he is brave and deserving of One For All, and then miraculously, Izuku's body glows with the power of One For All, coursing through his veins once more. All Might says it's a miracle, but perhaps the predecessors willed it for Izuku to hold this power. All Might then thanks his master Nana as well as the predecessors for returning One For All back to Deku. All Might takes both boys to be healed. Later, Katsuki wakes up in the infirmary next to Recovery Girl, with no recollection of ever using the One for All.
Elsewhere on Nabu Island, using a Warping Quirk, Tomura Shigaraki appears in front of a beaten Nine and confronts him. He managed to survive the attack of Izuku and Katsuki, which blasted him away from the battlefield, but now he can barely crawl away to escape due to his injuries and disease. Tomura tells him that he will fulfill his dream of a perfect society and Nine replies it only takes one leader. Tomura silences him by putting his hand on Nine's face and saying that leader will be him. Then he kills Nine with his Decay Quirk and leaves the island.