Six months remain before graduation, the deadline by which the yellow, tentacled, and supremely fast creature known as Koro-sensei has promised to destroy the Earth. His students, the misfits of Class 3-E at the prestigious Kunugigaoka High School, are also his dedicated assassins, though their efforts to claim the ten billion yen bounty have so far failed. The students find their resolve tested when a ruthless government-hired sniper codenamed Red Eye arrives, intending to eliminate their target by any means necessary. Despite this pressure, the students fail to land a killing blow during the school festival, but a far greater shock awaits them.

Classmate Kaede Kayano suddenly reveals her own hidden tentacles and launches a fierce personal attack on Koro-sensei. She confesses that her true name is Akari Yukimura, the younger sister of Aguri Yukimura, the teacher who previously inspired Koro-sensei to take on this role. Believing the creature murdered her sister, Akari has secretly trained for revenge. However, the artificial tentacles implanted within her are devouring her life force. In a desperate gamble, Nagisa Shiota, the class's most observant and naturally gifted assassin, gets past her defenses and kisses her, creating an opening to disable her tentacles and save her life.

With the immediate crisis over, Koro-sensei finally reveals his own tragic past. He was once a legendary human assassin known only as the Reaper. Captured by a rogue military scientist, Dr. Kotaro Yanagisawa, he was used as a test subject for an experimental serum that transformed him into his current form. It was Yanagisawa’s fiancée, Aguri, who treated him with kindness and showed him the value of being a teacher. When the experiment went catastrophically wrong, destroying the moon, Yanagisawa ordered the test subject’s termination. Aguri sacrificed herself to save the Reaper, and in her final moments, she made him promise to teach her class of struggling students.

Moved by this story, Nagisa refuses to accept that killing Koro-sensei is the only option. He leads a faction of the class in a plan to steal research data from Yanagisawa to create an antidote. However, the government has its own contingency: a deadly satellite laser set to fire on graduation day if the students fail. The class is captured to prevent them from interfering, but with the help of their handlers, Tadaomi Karasuma and Irina Jelavic, they escape. Returning to the classroom, they discover they have been tricked by a now-monstrously transformed Yanagisawa, who savagely defeats Koro-sensei and nearly kills Akari. Enraged by the repetition of the tragedy that claimed Aguri, Koro-sensei unleashes his full power to obliterate his former tormentor. He then uses a perfected surgical technique, developed in memory of his failure to save Aguri, to heal her sister.

With his final act of teaching complete, Koro-sensei submits to his fate. As the sun rises on graduation day, the students, united in tears, stand before him. Nagisa is chosen to deliver the final blow, using a specialized anti-sensei knife. Years later, the epilogue shows the students have grown up, each applying the lessons of their unique classroom to their lives. Nagisa Shiota, following in the footsteps of the teacher who changed him, has become a homeroom instructor himself, now guiding a new generation of troubled students from the front of the class.