The story revolves around a network game called "The World". It takes place four years after the "Twilight" incident (from the PS2 game), which not only shook the game world, but also the real world.
CyberConnect Corporation (CC Corporation), the creator and operator of The World, held a "Limited Edition Character" campaign for The World players and participants. The prize of the campaign is the Limited Edition Character itself: the legendary "Kite" and "Black Rose" from the ".hackers" data that was prohibited since the Twilight incident.
A pair of twin brother and sister in 2nd year junior high, Shuugo (the elder brother), and Rena (the younger sister), successfully obtained the Legendary Characters from the campaign. Shuugo who wanted to quit playing the network game, once again had to set foot into The World under his sister's invitation.
In the game world, Shuugo and Rena met other players, Mileyu and Houka and they quickly became close friends after several events and encounters. However, the seemingly peaceful game world began to meet with many weird changes resembled to the incident four years ago. But this time, Shuugo, Rena and their new friends are involved in it...