A group of National Guard trainees find themselves battling against a vicious group of mutants on their last day of training in the desert.
Rated R for prolonged sequences of strong gruesome horror violence and gore, a rape and language.
The film opens with a brutal scene of a restrained woman giving birth; she is then killed by a mutant (Papa Hades). There follows a synopsis of the previous movie, explaining that electronic surveillance was ordered to be installed in the New Mexico military base. The scientists are then shown working on the electronic surveillance installation, encountering problems with rats chewing the insulation on their power cables. Some 'false' readings are seen before the system fails. The antagonists are introduced at this point, and the scientists and their colonels are depicted meeting various untimely and gruesome ends.
Next, the film cuts to an apparent military operation in Kandahar, Afghanistan. The troops are depicted as lacking unit cohesion and showing individual weaknesses. The operation ends when a 'civilian' woman approaches the group and reveals multiple grenades under her garment; at this point, the operation is revealed as a training exercise for rookie troops on US soil. The sergeant lambastes the troops for their failure, then tells them they are going on a mission to bring supplies to scientists working on a surveillance system in a top secret area. By this time, many of the individual characters have been developed; we know that Napoleon is actually anti-war and that Crank is particularly gung-ho and violent.
Upon arriving at the secret base, the soldiers find no sign of the scientists. A garbled radio message is received, followed by a mirror signal from atop a hill. The sergeant orders a search-and-rescue mission; after questioning this order, Napoleon is left behind with Amber to monitor the radio. As they are climbing, Mickey falls into an old mine shaft, twisting his ankle in the process; he is pulled out by the sergeant, who orders him back to base. Napoleon and Amber discover a man, one of the missing scientists, trying to escape from the chemical latrine; he dies of a massive infection after warning them of danger. Soon afterward, they discover their transport vehicle in flames and their rifles missing. Amber starts up the hill towards the others but is attacked by one of the mutants. Mickey is returning down the hill and shoots the mutant in the shoulder from long range, and it disappears down a hole. Mickey gets a bit closer to Amber before a hand appears from underground and drags him gruesomely down the hole. Napoleon and Amber retrieve his weapon and set off to join the others, who by now have scaled a cliff and set up a rope after discovering the body of a second scientist.
Just as Amber and Napoleon join the main group, they are attacked by another mutant, and Spitter accidentally shoots and kills the sergeant. They decide to turn back, and Spitter volunteers to carry the sergeant's body down the rope abseil, since he feels responsible for his death. He falls before reaching the bottom, and it is revealed that the rope has been cut. The group then goes in search of another route down the cliff. They find a dead scientist and the mortally wounded colonel. He tells them what he knows of the mutants, including the fact that they keep the female victims alive for breeding, and says the only exit is through the mines. He then commits suicide with a pistol.
Two of the female soldiers lay a trap for the mutants, one of whom is successfully lured out and shot dead. However, while this brief victory is being celebrated, Missy is abducted by another mutant who has been camouflaged against the rocks. The group give chase into the mines, but Stump will not follow and decides to climb alone down the cliff and bring help. The others continue, under the leadership of Delmar, onwards and downwards through corrugated iron tunnels and mine shafts. Napoleon and Amber become separated after falling through a hidden shaft. Meanwhile, Stump, who has been climbing down the mountain, is attacked and killed by a mutant.
The captive Missy is carried to a room with makeshift furniture and nearly assaulted by the chameleon mutant, but fights it off, biting off part of its elongated tongue. As she tries to escape, Papa Hades enters the room and beats both her and the chameleon mutant and forcing him out of the room. He then proceeds to beat and rape Missy, and her screams alert the others, who are searching the mine for her.
Meanwhile, the fleeing chameleon meets and attacks Napoleon and Amber, who manage to kill him using a large rock. A blind mutant armed with one of the missing rifles detects the dead chameleon, and Amber and Napoleon retreat down a shaft into the lair of an apparently passive mutant - possibly the product of a mating with a non-mutated female. The remaining National Guard troops (Delmar and Crank) approach and Crank empties his magazine into the blind mutant, killing him, but not before the mutant shoots Delmar. Delmar claims it is only a shoulder wound and carries on. Napoleon appears and shows them the secret passage and th