The story takes place in the "ideal" and perfect city known as "No.6".

Shion, a boy raised in the elite and privileged environment of his home, gives shelter to another boy, who only gives his name as Nezumi ("Rat") on the former's 12th birthday.

What Shion soon discovers is how drastically life will change after meeting with the mysterious Nezumi, in whom he had saved one unforgettable, stormy night.