Tsukiyama is defeated by Touka with Kaneki and Nishio’s help, but the recent developments in the 20th ward draw the attention of the police, who sends two of their investigators, Kureo Mado and Kōtarō Amon to hunt down all ghouls in the area.
Intending to consume Kaneki himself, Tsukiyama prepares another trap for him, using Nishio’s human girlfriend as a hostage.
A ghoul named Tsukiyama approaches Kaneki with unknown intentions and the two start hanging out. However, Kaneki does not know that Tsukiyama is preparing a mortal trap for him.
After saving his friend, Kaneki is taken in by Yoshimura, a ghoul who run the Cafe “Anteiku”, who teaches him to blend in human society while hiding his true nature. However, he gets bullied by another ghoul named Touka.
Kaneki struggles to adapt to his new nature with no success, until another ghoul, Nishiki Nishio attempts to prey on his friend Hideyoshi Nagachika and he must fight to protect him.
Ken Kaneki is a young man who befriends the beautiful and enigmatic Rize Kamishiro, unaware that she is a ghoul. Rize reveals her intentions to eat Kaneki but by a stroke of luck Kaneki survives her attack but is mortally wounded. He is saved by an emergency operation, transferring Rize’s organs into himself. This subsequently turns him into a half-ghoul half-human hybrid and Kaneki struggles to survive and cope by himself.
Boros continues to fight with Saitama, which leads to Boros losing an arm. The fight continues on, even reaching the point where Saitama finds himself on the moon, but he quickly returns. Meanwhile, Mumen Rider, Stinger, and Lightning Max rescue the last of the City A survivors. The fight between the heroes and Melzargard concludes when Bang recovers and destroys his final marble, killing him. The fight between Saitama and Boros continues and it is revealed that Boros has regenerative powers. Eventually, they are both forced to use their most powerful moves. Saitama emerges victorious, and Boros admits he was not even close to Saitama. After the fight, Drive Knight warns Genos that Metal Knight is his enemy. Amai Mask appears and blames the S-class heroes for the destruction of City A, nearly causing a fight which is interrupted by Metal Knight who emerges to salvage parts of the ship. Meanwhile, Superalloy Blackluster discovers alien survivors whom Amai Mask promptly executes. Genos sees his past self in Amai Mask. Saitama emerges from the ship to find Tornado having a tantrum, and Genos quickly begins an argument with her; Bang interrupts before it can escalate into a fight. The parts Metal Knight salvages from the ship are used to rebuild the hero HQ which takes the place of City A which is wiped off the map. The A and S Class heroes are invited to stay in the newly rebuilt hero HQ. In the post-credits, Saitama destroys Pluton: King of the Underworld with one punch, much to his irritation.
Geryuganshoop complains about Groribas’ defeat as he and Melzargard are the only ELITE fighters left on the ship. Boros walks in and Geryuganshoop informs Lord Boros that the ship is badly damaged by the human intruder but Lord Boros tells him not to fear as the sphere keeping them safe won’t allow that to happen. Meanwhile, below the ship, Puri Puri Prisoner’s efforts were futile as Melzargard simply regenerates back into his form. Iaian tells the other heroes that it is pointless to keep trying. Melzargard tells his other head to go and contact the ship for a bombardment. As the head flies away, Metal Bat smacks him down. Melzargard and Geryuganshoop telepathically tell each other that both sides are dealing with big trouble as Saitama reaches another door. Atomic Samurai, Puri Puri Prisoner and Bang join forces and attack Melzargard together as Iaian tells them once more that direct hits have no effect on it. He tells them to retreat and think of a better way to handle the situation. Atomic Samurai, Puri Puri Prisoner, Bang and Metal Bat keeps attacking Melzargard telling Iai it is the only thing they know. Melzargard and Genryuganshoop again speak telepathically saying the life forms below are persistently attacking him and requested for a cleansing bombardment. Genryuganshoop is too busy but notifies the artillery crew. Genryuganshoop leaves the conversation and while Melzargard was distracted, Metal Bat finds a marble within Melzargard before he could regenerate thus destroying the marble and part of Melzargard for good. Genryuganshoop tries to lead Saitama out of the ship and Saitama went the opposite direction to find the controls room. He finally finds Genryuganshoop who has incredible telepathic powers that can manipulate everything and anything but in the end Saitama throws a pebble at him that destroys Genryuganshoop. After busting the other heads, the four heroes look up with shell bombardment ready to attack. After it shoots, Tatsumaki appears and stops the bullets in mid air, cursing the other four heroes fighting Melzargard. She then turns the bullets and forces them back onto the ship full force. Mumen Rider helps evacuate a victim to safety, when Stinger and Lightning Max appear wanting to help too. Bang on the other hand finds another marble and crushes it. Angry, Melzargard slaps the concrete along with Bang, who takes a direct hit. He sticks on a building, unconscious. With one more head left, Melzargard threatens to crush Atomic Samurai’s head and he retaliates after seeing his comrade in that condition. Saitama finds Boros who scans him for power, saying Saitama is Earth’s strongest warrior with limitless energy. Boros treats Saitama with respect and tells him his name and the prophecy that brought the Dominator of the Universe to Earth. Saitama punches Boros after being annoyed with what he heard, telling him he can’t attack other planets just to liven up his boring life. Boros’ armor used to seal in his immense power breaks apart and his true form emerges.
The Ancient King of the Terror Lizard Clan appears and Tatsumaki is sent to deal with him. After a short quarrel, Tatsumaki sends a meteor from outer space to destroy the monster. At Bang’s dojo, Bang tells Saitama and Genos, who were called there by Bang to learn some moves, about how his former best student, Garo, went wild and defeated all of his other top students. Suddenly, a Hero Association member comes and informs the heroes that an emergency has been declared and all S Class heroes have been called to a meeting. At the association, Saitama meets Atomic Samurai, an arrogant S Class hero, and others S Class heroes like Puri-Puri Prisoner, Metal Bat, Tanktop Master, Flashy Flash, Watchdog Man, Superalloy Blackluster, Pig God, Drive Knight, Zombieman, King, and Child Emperor. Sitch, a member of the associations, starts the meeting by telling the heroes that the emergency would be perilous and even with their skills, there is no guarantee of survival. Also, the great seer, Madame Shibabawa, had died while becoming agitated and choking on a cough pill because of a coughing fit while predicting the future. Sitch mentions that Shibabawa’s predictions have always been 100% accurate, be it monster attacks or natural disasters. Before she died, she left a note, thought to be her greatest prophecy. The note read “The Earth is in trouble”, alarming the heroes. He warns the heroes to prepare for a fight in the next 6 months. Just after he says this, the HQ is attacked by the Skyfolk led by Sky King, who are quickly slain by Melzalgald, a member of an alien race called the Dark Matter Thieves. An alien spacecraft then proceeds to destroy City A, causing a large number of casualties as their alien invasion begins. Just as Melzalgald is about to kill some City A civilians, Iairon, a student of Atomic Samurai, arrives and engages him in battle. Saitama encounters the alien ship and advances towards it, avoiding some projectiles thrown at him and damaging the ship. Meanwhile, Melzalgald proves to be a challenge for Iaian and causes him to lose his left arm before Atomic Samurai intervenes, saving his student from death. Melzalgald, however, regenerates and the heroes’ attacks seem to cause no damage to him. Then, Metal Bat, Bang and Puri Puri Prisoner arrives. Puri Puri Prisoner enters Angel style and attacks Melzalgald. Elsewhere, the other S Class heroes discuss how to bring down the ship. As they offer differing views, Genos notes that Saitama has already entered the ship and slain a large number of the aliens. He comments that there is no evil that Saitama is unable to defeat. Saitama encounters Goribas, an alien, bragging how to defeat him. But is slain, as Saitama punches at everything and continues to destroy the ship, wondering where the boss might be. At the end, Boros is seen on his throne.