In the year 2005, a computer virus called Pluto Kiss completely shuts down and restricts the global internet network. In 2007, after extensive rescinding of the network, an online network game (MMORPG) called The World is created and released.

Tsukasa suddenly awakens to find himself in The World, being able to feel, smell, touch, see and hear everything as if he was really there. He attempts to log out but fails to do so. Being unable to remember what has happened before he awoke, he wanders around aimlessly to find answers. While doing so, system moderators, the Scarlet Knights, suspect that he has been working with hackers, because of a tweaked cat-faced character he had been seen with. Tsukasa finds a magical item, that grants him the power to use the fearful Guardian that will protect him from any harm. To Tsukasa's dismay it turns out that this guardian can not only easily defeat player characters in the game, but actually badly hurt players in the real world.

On his search for truth, Tsukasa encounters the friendly and supportive Mimiru, the wise, fatherly Bear, the manipulative BT, the unscrupulous Sora, the fun-loving Crim, and the mysterious Subaru, leader of the Scarlet Knights. When a mythical item called the Key of the Twilight turns out to be less of a myth, Tsukasa, questions whom he can really trust, and what the power to overcome The World's system limitations actually entails...

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Sequel: .hack//Liminality
Same setting: .hack//Roots
Same setting: .hack//Quantum