CyberConnect Corporation (CC Corporation), the creator and operator of the network game The World, holds a special campaign for its players. The grand prizes are two Limited Edition Characters: the legendary Twin Blade, Kite and the Heavy Blade, Black Rose from the .hackers data that has been prohibited since the Twilight incident.

The second-year junior high school twins, Kunisaki Shuugo, and Rena, successfully win the Legendary Characters from the campaign. And even though Shuugo never played the network game before, he sets foot into The World on his sister's invitation.

In the game world, Shuugo and Rena meet other players, like The Rare Hunter of Love and Courage Mireille a Wavemaster, the Werewolf Ouka of the Divine Fist, and the shy Wavemaster Hotaru and quickly become close friends after several events and encounters. However, the seemingly peaceful game world begins to show signs of weird glitches that eerily resemble the incidents from four years ago. Only this time, Shuugo, Rina and their new friends are involved in them...

Note: Set in The World, four years after the Twilight incident (from the PS2 game), which not only shook the game world, but also the real world.

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Prequel: .hack//Liminality
Same setting: .hack//Gift