A computer virus by which AutoReivs become self-aware, similar in nature to the concept of rampancy in the Marathon Trilogy series of computer games. It is possible that the Cogito Virus is distributed and/or controlled by Proxies: AutoReivs of all kinds exhibit odd behavior (prayerful postures, attacks on humans) in the presence of both Monad and Ergo Proxy. Indeed, following a close encounter with Monad Proxy in the Romdeau Shopping Mall, Pino appeared suddenly stricken by the same prayerful pose that afflicted other AutoReives throughout the series; shortly thereafter, AutoReive engineers were instructed to hunt her down, citing Cogito infection as their motive. It is also mentioned that the Cogito Virus is a potential offshoot of the Boomerang Project.
Most of the Ergo Proxy series is an examination of what it means to be human. The phrase "Cogito, Ergo Sum" (I think, therefore I am) is the basis of the entire series. The cogito virus is named such because it causes the machines to be self aware and exhibit all the foibles and strengths of human emotion. This accounts for the different behaviors/reactions when the machines become human - they become as unique and distinct as a human. The praying position is most likely connected to humanity's singular desire to create/find a faith in a higher deity - unique among the animal kingdom and very distinctly human.
AutoReivs infected by the Cogito Virus are said to develop human emotions and a soul. They can no longer be controlled by humans and have been known to turn violently on their masters. Effects of self-awareness differ between individual AutoReivs for reasons unknown: Pino, for example, was self-aware for the majority of her screen-time, but she never attempted to harm anyone. Iggy, too, was purportedly self-aware for some time, but he only attacked other humans after suffering the equivalent of a mental breakdown (proximate cause for this breakdown was Re-l Mayer's rejection of him). As such, it is possible that the presence of Re-l Mayer as Iggy's raison d'etre kept Iggy stable. Under other circumstances, infected AutoReivs become immediately violent, such as the skirmish in Daedalus' lab when Re-l was "killed" by two AutoReivs that had been intentionally infected with the "weaponized" virus and had become highly aggressive. Different theories exist to account for these discrepancies: multiple versions of the Cogito Virus might exist; or the virus might affect different AutoReivs in different ways, depending on their background and programming.
(As in the story, the character Pino is said to have developed the Cogito Virus.)
The Cogito Virus is said to be part of the Boomerang Project, but the precise cause of it is unknown.
One suggested reason that was proposed for the creation of the Cogito Virus is that it might be a final contingency plan for rebuilding the Earth for the humans who left for space. If the proxies were incapable of the task, they were to produce humans who could aid them. If this failed, then the AutoReivs could continue the task, now sentient and understanding of their goal.