The film opens with the Military of Japan's failed attempt to capture whoever it is that has destroyed half of the Moon, which sees the death of the entire squad sent to capture it. Meanwhile, Nagisa Shiota, a ninth-grade student of Kunugigaoka Junior High School, narrates of how he came to be sent to the situation he is in: he is included in Class 3-E, which is reserved for delinquents and other undesirables of the school and is a laughing stock among the school. However, Class 3-E is actually a cover up for the Government of Japan in their attempt to assassinate Koro-sensei, a tentacled creature apparently responsible for the Moon's destruction. The students have to assassinate him before graduation using either a special knife or BB gun, the time when he plans to destroy Earth, but at the same time also have to study both academic and assassination disciples from him. In teaching, Koro-sensei is assisted by the government-affiliated Tadaomi Karasuma and Irina Jelavić, a Serbs assassin.