This story is in six chapters. The chapters are of varying lengths and structures, but they all cover July 2012 from different perspectives.
The story begins in the first chapter, Down the Rabbit Hole, on July 12, 2012. Minaki Yuki lives a peaceful everyday life with Tsukasa and Kagami, her childhood friends, when one day she meets a mysterious girl, Takashima Zakuro (a girl from another class in Yuki’s school, which she seems to have met before, but Yuki doesn’t remember that).
The next day, she finds out that Takashima Zakuro committed suicide. There are rumors at school about predicting the end of the world in 2012 - one of which is a website called the "Web Bot Project", a network designed to use the "collective unconsciousness" for its calculations.
A boy in Yuki's class named Mamiya Takuji gets up and makes apocalyptic predictions that the world will end on the 20th, that Zakuro's death was the first sign. He talks about an event called "Last Heaven", where the world will be destroyed and reborn.
As time goes on, and more and more deaths, the prophetic date is getting closer and closer, while Yuki attempts to get to the bottom of the true goals of Mamiya Takuji, the Project Web Bot website and the Last Heaven event.