Class 3-E is getting ready for their class trip to Kyoto, and Koro-sensei is as excited as ever! Nagisa is in a group with Kaede, Karma, Tomohito, Manami, and the class idol Yukiko Kanzaki. The students are aware of the fact that this is a great opportunity to assassinate Koro-sensei, but they cannot help having great time with him. However, the trip becomes even more exciting and dangerous when they get attacked by a bunch of delinquents who kidnap the girls. As if that is not enough, there is a hired sniper named Red Eye lurking around, ready to be the one who would assassinate Koro-sensei and claim the prize. Can the students of Class 3-E rely on Koro-sensei even now?

A mysterious creature destroys 70% of the moon. The creature then warns that if he is not destroyed by March of next year, Earth will be next. The creature also demands that he becomes the homeroom teacher for 3rd grade E class at Kunugigaoka Junior High School. The government is powerless to say no. The creature then becomes the homeroom teacher of 3rd grade E class which consists of failed students including Nagisa Shiota (Ryosuke Yamada). The creature is called Teacher Koro. Meanwhile, the government requests that the students try to kill Teacher Koro even though he possesses super powers. The government offers a 10 billion yen reward for whomever successfully kills him. The students are confused by the situation, but decide to kill Teacher Koro. When their class begins with Teacher Koro, the students finds themselves having a good time with their new teacher.