Two years after the world as we know it has ended, Shizuru leads an uneventful life in her hometown of Agano. But one day, she finds a clue that will lead her on a journey into the unknown to find her missing friend.

As the train continues on its journey to Ikebukuro, each new stop begins to take weirder, wilder turns. Meanwhile, Akira appears to be hiding something from the others.

Shizuru and Reimi find themselves prisoners near Inariyama Park. They must escape their tiny captors, and find a doctor to cure Akira's affliction before it's too late.

Reimi is excited to head into Oizumi-gakuen, which has transformed into her favorite anime. However, they're met with a much bleaker retelling where the bad guys reign supreme.

Poison Pontaro sets off on an armored train with Yoka in tow. The fate of the world now rides on Shizuru and the gang, in hot pursuit aboard the Apogee.