A captive woman, forced to breed mutant children, is unable to provide healthy offspring after giving birth to a stillborn and is killed by Papa Hades, leader of the inbred mutant clan living at a nuclear testing village in the New Mexico desert, designated as Sector 16. Following the events of the first film, the United States Department of Defense sent a military army to occupy the location and exterminate the remainder of the mutant clan. Colonel Lincoln Redding and a trio of scientists who are working in that area on installing a surveillance system are attacked by the mutants.

Later, You and the group of National Guardsmen in training led by Sergeant Jeffrey "Sarge" Millstone are sent into the desert to resupply the scientists. They arrive to find the base camp abandoned after the mutants' attack. When the soldiers pick up a faint distress call, Sarge organizes a search and rescue mission through the hills. You are a Private First Class that being group with Private First Class Amber "Barbie" Johnson, Private First Class Marisol "Missy" Martinez, and Private First Class Delmar "Del" Reed to go in the other side of the hills. While Sergeant Jeff "Sarge" Millstone, Private First Class Carlos "Crank" Medina, Private First Class David "Napoleon" Napoli, Private First Class Michael "Mickey" Elrod, and Private First Class Scott "Stump" Locke are going to the main path of the hills. You carry your rifle as you exploring with your group in the side of the hills.