Area 51 is the only action-packed 1st person shooter set in the U. S. governments most secret and secure military facility. 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 led Specialist Ethan Cole of HAZMAT (hazardous materials) Division is sent to investigate. As Cole, players will delve into five massive levels within the confines of Area 51, discover a mutagenic side effect of the virus that controls the minds of those infected, as well as an ancient alien colony buried beneath the facility. With a multitude of human and alien weapons, players must explore chilling conspiracies such as the extraterrestrial crash at Roswell and the faked lunar landing, in order to solve the enigmas of Area 51 before the viral mutagen is released and irrevocably mutates all life on earth.

In July 1947, an alien spacecraft crashed near Roswell, New Mexico in the United States. The craft was recovered by the U. S. Air Force and taken to Area 51 in Nevada, where the lone survivor of the crash, a powerful Grey named Edgar, was held captive by the U. S. military. Eventually, the Greys opened a dialogue with the Illuminati led by the ominous Mr. White (Phil Proctor), and struck a deal with them. The Illuminati would give the Greys a research base 3 miles below the surface of Area 51, the use of the base as a landing site, and give them human test subjects where they, along with human scientists, would research a mutagenic virus to use in a war on their homeworld. In return the Greys would give the Illuminati exclusive access to Grey technology. The Illuminati used some of this technology to spy on the population. The Greys and the human scientists eventually developed a powerful alien being - known as the "Theta", which spread the virus. Unbeknownst to many of the scientists working on the project, the Greys and the Illuminati were also planning to use the virus against the Earth population and dominate the planet. When Dr. Winston Cray found out about the plan, he let loose the "Theta" and the mutagenic virus throughout Area 51, in an effort to slow them down. This prompted the military to send in a Quick Reaction Force led by Major Bridges (Powers Boothe) to quarantine and contain the virus. HAZMAT Team Delta, the first team initially sent into Area 51 are ambushed by the "Theta" creature, sustaining casualties, before withdrawing deeper into the base. HAZMAT Team Bravo, composed of team leader Ramirez, McCan, Crispy, and mission specialist Ethan Cole is sent to find Delta.