The story begins in a futuristic domed city called Romdeau, built to protect its citizens after a global ecological disaster thousands of years prior. In this utopia, humans and androids known as AutoReivs coexist peacefully under a total management system. A series of murders committed by robots and AutoReivs infected with the Cogito virus (which causes them to become self-aware) begins to threaten the delicate balance of Romdeau’s social order. Behind the scenes, the government has been conducting secret experiments on a mysterious humanoid life form called a “Proxy.” The Proxy beings (described as almighty, god-like, immortal, omnipotent) are believed 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 is assigned to investigate some of the murders with her AutoReiv partner, Iggy. She encounters two unknown and highly powerful creatures. She later learns that a Proxy was involved. The other central character, an immigrant named Vincent Law, is revealed to be connected in some ways with this Proxy. After being hunted down, Vincent lives in a commune on the outside of the dome for a while. 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 as well as the people inhabiting them who are created in special incubators.