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 (Marilyn Manson), 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 (Ian Abercrombie) 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 is ambushed by the “Theta” creature, sustaining casualties, before withdrawing deeper into the base. HAZMAT Team Bravo, composed of team leader Ramirez, McCann, Crispy, and mission specialist Ethan Cole (David Duchovny) is sent to find Delta.