At this point, however, Jun began to get cold feet. He knew a great deal about the previous history of The World, including the struggles with Morganna. A rogue entity known as Cubia, the anti-existence, had arisen as a means to counterbalance the great power of the infamous Twilight Bracelet. Jun was concerned that the imbalance of power presented by the Epitaph PCs would create an anti-existence. He did a bit of clandestine investigation and discovered evidence that an anti-existence even more powerful than the previous one was being created. He brought his concerns to Jyotaro, asking him to hold off on the R.A. Plan until they could find some way to keep the anti-existence under control or even nullify it, but Jyotaro laughed and claimed that there was no such thing. From his actions of late, Jun had begun to notice a certain mania to Jyotaro's actions. It seemed that Jyotaro was more obsessed with surpassing Harald than anything else, and that he would go through with the RA Plan with little regard to safety or risk. Rather afraid of Jyotaro by this point, Jun did the only thing he could think of that would stall the Plan: he secretly stole the Epitaph PC of the seventh Phase, Tarvos the Avenger, and hid it away on his computer.

However, Jyotaro was not called the genius of his age for nothing. He had begun to suspect Jun of treachery, and had prepared for such an occasion. He presented a backup plan, consisting of a dummy Epitaph PC for himself to use in place of Tarvos and its now useless Chosen One. With a now "complete" roster of Epitaph PCs, he began the execution of the RA Plan in earnest. Unfortunately, the RA Plan failed to get off the ground. To prevent the birth of the new anti-existence once and for all, Jun set a fire that quickly consumed the C3 building. Due to the fires, 80% of The World's data was lost, and six of the involved Epitaphs escaped into the game data. Accepting all responsibility for the incident, Jun disappeared from the public eye. Unable to accept that someone he had believed in so strongly could simply abandon their vision - and thus leave his own vision unfulfilled - Jyotaro began to question Jun's motives and actions so much that he drove himself insane.

Of course, nobody knew or cared what happened to the Dummy Epitaph PC. It was just a placeholder, after all. Or was it? By the end, Jyotaro believed himself to be superior to Harald, who had managed to immortalize himself within the previous version of The World after a fashion. Jyotaro's goal was the same - or for himself to become the new "God" to manage the system in place of an AI. Jun believed that there was no place for technology without a heart, and that Jyotaro's failure came about because he did not "love" The World. Jyotaro disappeared from the history of C3 as well...

Merging the remaining game data with another one of their projects, C3 created The World R:2. At first it was rather buggy, but slowly C3 began to work out patches to help the system work. Unfortunately, strange issues beyond simple bugs began to arise. A mysterious entity consisting of fluid black dots, a character who could put PCs into comas by killing them in-game, and a mysterious player with an arm bound in a metal container... this was all part of the legacy that Jun left for his sister, Reiko Saeki. Determining that she was the chosen one of Tarvos, he sent her all his information and evidence, beseeching her to try to get to the bottom of the strange events and work to help stabilize The World once and for all. Upon learning of the story she took up his mantle, hiding her relationship to her brother so that she would be hired at C3 and recover the Tarvos Epitaph PC. With her newly-made Epitaph PC, Pi, she started working with C3's own internal Security Department, Safety Division 2 under an individual she knew only as "Kazumi", before she was transferred to something called Project GU, who worked solely with investigating the strange phenomena beleaguering The World.