The U.S. Army has received a distress signal from Area 51 where a viral outbreak has just shut down the research facility and the automated quarantine procedures have locked all scientific and military personnel inside. A small Special Forces unit including Specialist Ethan Cole of the HAZMAT (hazardous materials) Division is sent to investigate.

As Cole, players delve into the massive levels within the confines of Area 51, only to discover a deadly mutagenic side effect of the virus that controls the minds of those infected, as well as an ancient alien colony buried beneath the facility. Players will uncover the truth behind chilling conspiracies as they come across the remnants of the extraterrestrial crash at Roswell, alien autopsies, and the faked lunar landing. Cole must solve the enigma of Area 51 before the viral mutagen is released and irrevocably mutates all life on Earth.