The story takes place in the year 2020, just three years after the events of .hack//G.U.. The story will take place not only in the new version of "The World" known as "The World R:X" 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 Saika Amagi transfers to his school. She takes Tokio to the school rooftop one day and sends his consciousness and real body into The World R:X, where Tokio begins to discover that time for some characters, and even the history of The World itself, are going haywire; for instance, Tsukasa is turning back into his previous cold mannerisms, and Haseo is being cold-hearted and obsessive about finding and killing Tri-Edge.
It has also been revealed from a hidden poem on CyberConnect2's website that Kite from the original four .hack games and Haseo from .hack//G.U. will be returning. According to the group picture set along side the logo on the home page of the official site, other characters such as Azure Kite, Atoli, Tabby, and Ovan will also make appearance.
