.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. 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. 3: Redemption
By Redemption Yata is forcibly removed from the Serpent of Lore by CC Corp Executives and replaced with Sakaki, after promising CC Corp to remove the threat of AIDA against the greater networks. Sakaki forces Haseo into a PK tournament that is corrupted by AIDA. Haseo has no choice but to fight in the tournament and defeat Sakaki. Later, Haseo and the others find Yata who is revealed as the seventh Epitaph user with Ovan being the eighth.
Bo meets Ovan's sister, Aina, which leads Ovan to inviting Haseo to another fight. Haseo goes to the area with G.U. and defeat him. After the battle Ovan uses his Avatar's special ability known as "The Rebirth" and completely resets the Internet and cleanse it of AIDA. The G.U. members are saved by Zelkova, leader of Moon Tree, who reveals that Ovan's actions caused several comatose players to wake up. The other unconscious player's minds still lie within The World and Yata discovers a creature named Cubia that is trying to devour the game, resulting in the death of all players.
Haseo uses his Avatar powers to summon the goddess Aura who hints to them that the key to defeating Cubia is the eight Avatars. Since Haseo has defeated all of the others Avatars in battle, he possesses the key to defeat Cubia who starts destroying The World. Haseo requests all the players' help to defeat Cubia's remnants as G.U. and Zelkova locate the main body. Fighting Cubia, Haseo uses all of his Avatar's powers to destroy Cubia and is aided by the mysterious short reappearance of Ovan.
With Cubia destroyed, all the remaining comatose players awake with Haseo meeting Shino once again. Upon meeting her, Shino motivates Haseo to be more honest with his feelings which causes him to pursue Atoli who believed that Haseo would stay with Shino. A new ending is unlocked by passing the Forest of Pain sidequest in which Haseo is conceded the wish of having another conversation with Ovan; he later states Ovan will return.