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Following the disappearance of the Ultimate AI Aura, The World began to experience numerous bugs and problems. These problems were not contained to just The World, but eventually spread throughout the entire world network. Realizing that Aura was a crucial part of the network, CC Corp decided to try and bring Aura back, or failing that create a new Ultimate AI under their control. To this end, they hired two ingenious programmers, Jun Bansyoya and Jyotaro Amagi, to head a secret program known as "Project G.U.". Amagi eventually devised a plan he entitles the R.A. Plan, which was designed to create a new Ultimate A.I.
By salvaging the data of the Eight Phases of Morganna and sealing them into Epitaph PCs, Amagi hoped to recreate the program that had created Aura. Bansyoya, fearful that the experiment would create a new Cubia. secretly sabotaged it by stealing the Epitaph PC containing Tarvos. However Amagi had expected this, and produced a copy of Tarvos called a Dummy Epitaph User. Using this dummy, and the other seven Epitaph PCs Amagi attempted to recreate Aura. The plan was a catastrophic failure, and the shockwaves of the test resonated throughout The World, destroying large amounts of its data, it also caused a fire to start in CC Corp's headquarters. Furthermore the event caused all seven of the Epitaph Users to fall into comas, and drove Amagi insane. CC Corp quickly disbanded Project G.U., and Bansyoya also resigned, taking full responsibility for the incident. Unknown to CC Corp, he took the Epitaph PC containing Tarvos with him, and continued to observe The World on his own.
Two years after the R.A. Plan's failure, new problems began to plague The World R:2, a game made up of the remnants of The World's data. Wanting to find the source of these problems, CC Corp restored Project G.U. and hired Takumi Hino, a former .hacker to head it. To assist him, they assigned CC Corp employee Reiko Saeki to the project. Unbeknownest to CC Corp, Saeki was actually the sister of Jun Bansyoya, the former leader of Project G.U., and had been given the Epitaph PC for Tarvos by her brother.
Working through the characters Naobi and Ender, Hino and Saeki began investigating The World through the powerful guild TaN. They soon discovered a data anomaly in the character Ovan. Launching an elaborate trap, they were able to successfully capture Ovan, and began examining his PC Body. However, Ovan was able to escape by using a strange entity sealed inside his character's left arm. With Ovan gone, Hino and Saeki abandoned their former PCs and moved into the characters Yata and Pi. Using these bodies, they began searching for the other Epitaph PCs. The first one they located was Kuhn, the Epitaph PC for Magus.
As Haseo discovers the existence of AIDA, Kuhn and Yata make efforts to persuade him into joining Project G.U. and awakening his avatar -- much to Pi's dismay. They hope to defeat both Ovan & AIDA and restore peace to The World. As more and more PC's fall into comas, Yata becomes obsessed with AIDA and Haseo learns the truth behind Ovan.
After awakening his avatar through a fit of jealousy and rage, Yata is slowly brought back to his senses by Pi. Soon Ovan is defeated and Yata reveals to Haseo his past in The World and warns him of the upcoming danger as the anti-existence Cubia is reborn. He expresses his desire to finally fight at the frontline as he once did before and offers to join Haseo's party. When Cubia is defeated, Yata disbands Project G.U., but offers to continue playing with Haseo if needed.