Due to the fact that the Blacklight Virus infection revives 14 months later, spreading to the whole city rather than just Manhattan in the video game, Prototype, New York City is called New York Zero, and is divided into three zones to keep the virus in line.
- Green Zone: A peaceful zone.
- Yellow Zone: A quarantine zone under suppression by Blackwatch.
- Red Zone: A pure Hell zone of New York Zero overrun by the Blacklight Virus. This is where Alex Mercer resides