Modern day fears explode onto the streets of a small American town swarming with alien life. The government is desparate, struggling to contain secrets so terrible they can no longer be kept. You are Aeran Pierce, a Special Forces assassin thrown into one of the most explosive moments in American history. Everything hinges on your actions in BlackSite: Area 51.

The game begins with Captain Aeran Pierce and the rest of his Delta Force Echo Squad being sent to investigate a supposed weapons bunker in Iraq. They are accompanied by the head of an elite science team, Doctor Noa Weis. The bunker is infested with mutated humans and wildlife (referred to collectively as Xenos) created by an alien crystal found in the bunker. This crystal incapacitates Pierce and forces the squad to retreat.Three years later, a heavily armed militia has taken control of Area 51 and the surrounding area, accompanied by an outbreak of alien creatures identical to those encountered in Iraq. Echo Squad and Doctor Weis have been chosen to reclaim the base.