Each weapon has two modes of firing, the first being the primary method, while the second is of a much higher power level, at the cost of ammunition and accuracy to the player.

While in a mutant form, players can easily spot enemies, which would otherwise be cloaked to the regular human eye, albeit with a slight ocular defect.

The scanner, when equipped, adds a translucent bar to the player's HUD, which changes in color and height from light blue, to deep red.

Items which are scanned are viewable in-game, providing insight into the workings of Area 51, as well as proving necessary to unlocking secret videos made by Dr. Cray or Mr. White.

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.

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.

Making their way topside, the Illuminati disables the cargo elevator, killing Chew and leaving Cole bitten by one mutant, partially mutating him.

Able to switch between human and mutant form, Cole is guided deeper into the base by Edgar reanimating corpses to deliver information telepathically.

He meets Edgar miles beneath the surface who reveals the scientists used his DNA to create the virus, and the nature of the experiments at the base, which killed dozens of his species to harvest it.

Edgar gives Cole the cure to the mutagenic virus, and instructs him to destroy the Grey's ship, that is leaving with dozens of Theta duplicates.

Cole watches as a truck drives past, with a green, alien-like container on board with unknown contents inside and walks away from the site.