.hack//G.U. takes place in an alternate version of Earth in the year 2017. As depicted in the first .hack game series, the "2nd Network Crisis" was an incident that occurred seven years ago in which many computer systems across Japan malfunctioned. Through the efforts of those games' hero, Kite, the incident resulted in the birth of Aura, the ultimate artificial intelligence (AI), capable of making decisions for itself. Under the guidance of Aura, The World, the most popular massively multiplayer online role-playing game at the time, flourishes and the events of .hack//Legend of the Twilight occur during this four-year period.

In late 2014, Aura disappears, resulting in the slow decay of The World and the Internet as a whole. In response, the company that administrates The World, CC Corp, sets up "Project G.U." and tasks them with remedying the problem. They come up with the "Restore Aura (RA) Plan", in which they attempt to retrieve the fragments of Morganna—an AI that served as Aura's "mother"—and seal them into player characters (PCs) of The World. In theory, this would allow the Project G.U. programmers to manipulate the Morganna program to recreate Aura. Only certain "chosen" players could control these special "Epitaph PCs".

After locating candidates to operate the Epitaph PCs, the team proceeds to test the RA Plan despite concerns over "anti-existences" that might damage the Internet. The program fails catastrophically and destroys over 80% of the data for The World.[9] Instead of trying to salvage the data, CC Corp develops The World R:2 and releases it to a new generation of players. However, this new game is less popular than its predecessor and becomes plagued by "player killers" (PKs), players who target other players for fun and sport. The Epitaph PCs which had been lost during the RA Plan disaster resurface in the new version, attached to certain players of interest.

Vol. 2: Reminisce: In Reminisce, Haseo and the G.U. staff find themselves trapped inside the game, physically unable to leave or log out, or remove their hardware. Atoli recovers, but is rendered mute, able to communicate only through instant messages. Yata explains that AIDA has copied The World's server, trapping everyone inside to experiment on them. After cracking into the administrative control area, they transfer everyone back to CC Corp's servers. Shortly afterwards, Haseo is approached by Alkaid, concerned for Sirius, a player infected with AIDA. They enter into a tournament to fight Sirius, but Alkaid is ambushed by the AIDA-infected player Bordeaux, who leaves her in a coma. After learning that Sakubo is another Epitaph user, Haseo requests Endrance's assistance for the rest of the tournament. They defeat Sirius and purge him of his AIDA infection that contained Atoli's Epitaph.

With Atoli's Epitaph returning, she also recovers. However, her superior from the guild Moon Tree, Sakaki, causes Atoli to slide into a depressed fugue, and be used again by AIDA. Sakaki attacks his own guild, Moon Tree, in order to drive Atoli to the point where she will utilize her Avatar to actively support the AIDA infestation in order to control the real world through the Net, using AIDA as a cat's paw. Haseo liberates Atoli, removing her infection, and driving off Sakaki. Tracking Sakaki, Haseo defeats him after he purposely infects himself with AIDA in a last-ditch effort to gain control of the network. Following this, Ovan appears and reveals that he is Tri-Edge, infected in his left arm with AIDA. The enemy that Haseo believed was Tri-Edge was actually Azure Kite, one of three AIs that Aura had created to destroy the AIDAs.