- "Of the people involved in Project G.U., there was one man on the team who was absolutely invaluable, Jyotaro Amagi."
- — Jun Bansyoya —
Jyotaro Amagi (天城丈太郎) is the genius programmer responsible for the R.A. Plan.
CC Corporation to be one of the leaders for Project G.U. and help CC Corp. in their attempt to build a new Ultimate A.I.
He was paired up with Jun Bansyoya and together they wrote up the R.A. Plan. A plan in which the Eight Phases of Morganna would be sealed inside specially-created Epitaph PCs and used by players to recreate Aura. When Jun came forward with concerns that the plan might create a new Anti Existence, Amagi laughed it off.
Concerned by his attitude, Jun decided to sabotage the project and stole the Epitaph PC containing Tarvos. However, Amagi had created a special dummy program to substitute for it, and was able to proceed with the R.A. Program. The program was a complete disaster, and Amagi went insane, setting fire to CC Corp headquarters after which he uploaded himself into the network, while an AI counterpart of his own creation Geist would go on to continue his work.
Amagi's legacy would continue to live on in the form of a special program he created. This program, which would eventually become the groundwork for the game The World R:X, capable of physically inserting a player directly into the game. This copy would eventually fall into the possession of Tokio.
During half-through of the game, he was first mentioned by Saika as her brother and then by Pi who explained more about his background to Tokio during their mission in alternate 2017.
He first appeared when Tokio, Saika, and Cello confronted Geist for the last time and to rescue Klarinette. Geist revealed that Jyotaro is his master whom he had kept at his hideout as he had become catatonic. Geist explained that he intend to complete Jyotaro's research to create Immortal Dusk. Flugel interrupted that Jyotaro's plan had already failed and as the result, Amagi's mind was deteriorating. Geist won't listen to this until Jyotaro suddenly became a monster and then deleted Geist as he questioned his existence. However, this didn't last long as he crumbled into pieces of data but not before uttering his aunt's name, Ayaka, the moment he saw Saika. From Tokio and Saika's conversation afterwards, it was assumed that his consciousness could never return since Tokio apologized to Saika that he "cannot save her brother".
He's last seen laying in the hospital room with Saika and later visited by Tokio who had returned to the real world.
Three years after the events of .hack//Link, Amagi resides in what appears to be a psychiatric care facility where he is visited by Ryuuji Sogabe.