The story starts on February 6, 2036, when an accident involving computers going berserk destroys many large cities around the world. The massive disaster is named the "2036 Problem", but there's a prediction that there will be a similar incident in 2038. So a group of scientists use the Gaia Supercomputer to create an "Earth Simulator" to prevent it from happening, but fail because human birth potential has dropped dramatically.
The scientists then introduce the "Arecibo Message" formula to the Earth Simulator, successfully bringing mankind into another world. They are excited at first, until they realize that human beings in the Earth Simulator themselves created another Earth Simulator. The scientists begin to suspect that they are actually only the product of an Earth Simulator from creatures whose position is above them.
The story centers around Takaoka Pollon, a hacker who has the ability to "Save and Load" like in a video game. Using his Hacking Trigger System, he can intervene with the world line around him.