Two years have passed since the final battle with Sephiroth. Though Midgar, city of mako, city of prosperity, has been reduced to ruins, its people slowly but steadily walk the road to reconstruction. However, a mysterious illness called Geostigma torments them. With no cure in sight, it brings death to the afflicted, one after another, robbing the people of their fledgling hope.
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. 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.
Immediately before the events of The Matrix Reloaded, the crew of the hovercraft Osiris discovers a quarter of a million sentinels drilling through the surface of the earth towards the last human city of Zion. But can the Osiris survive long enough to warn Zion?
