The story takes place in the year 2020, just three years after the events of .hack//G.U. It not only takes place in the new version of "The World" known as "The World R:X", which has become popular, but in the real world as well. The lead character is a middle school student named Tokio Kuryuu. He lives a normal life as a gamer until a mysterious girl named Ayaka Amagi transfers to his school and takes him in the game world.