Tadaomi Karasuma, an agent sent from Japan's Ministry of Defense tasked with training Kunugigaoka Junior High School's Class 3-E, or so they call it "The End Class" to kill their octopus specimen teacher: Koro-Sensei. But now he was.. on summer vacation with his students..?

As a result of the bet Class E had with Class A, they had the opportunity to go on a special 3 day vacation on a small island, all financially suported by the school. With this, they planned an assassination on Koro-sensei. Unfortunately, the assassination attempt had failed even with all the weaknesses and strategizing, as Koro-sensei had a backup plan unbenknownst to anyone, leaving him vulnerable as a tiny ball with an indestructable shell.

With a tense mood, everyone returned to the restaurant by the beach, resting after their failed attempt. Suddenly, something unexpected happened, students left and right started feeling ill, rising temperatures, nosebleeds, fainting. This was no coincidence, this was an attack.

An unknown number called Karasuma's phone, demanding them to bring the vulnerable Koro-sensei to him in an hour, or else the students will perish to the artificial virus they were infected with. What could they do..??