A series of murders committed by AutoReivs infected with the Cogito virus (which causes them to become self-aware) begins to threaten the delicate balance of Romdeau City's social order. Behind the scenes, the government has been conducting secret experiments on a mysterious humanoid life form called "Proxy"; these Proxy beings (often described as god-like and immortal) are said to hold the very key to the survival of humanity.
Re-l (pronounced /riːˈɛl/ or "Ree-EL"; also represented by the spelling "R.E.A.L." in the Romdeau citizen database) Mayer, the Regent's granddaughter, is assigned to investigate the murders with her AutoReiv partner, Iggy. She encounters two unknown and highly powerful humanoids. She later learns that these humanoids are the Proxies. The other central character, an immigrant named Vincent Law, is revealed to be connected in some ways with the Proxies. After being hunted down, Vincent temporarily lives in a commune on the outside of the dome. During the massacre of the commune by Raul Creed of the Security Bureau, Vincent leaves the area for Mosk, his birthplace, in an attempt to recover his memories. Re-l later rejoins him to try to discover the truth behind the Proxies and the domes. It is revealed among other things that domes are all created by Proxies and cannot function without their presence within the domes.
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