Earth's natural resources have been exhausted by mankind and battle rages between the soldiers of four leading Corporations: the Capitol, Bauhaus, Mishima and Imperial.

Mitch Hunter (Thomas Jane) and Nathan Rooker, battle hardened Capitol soldiers, fight a desperate battle against a Bauhaus advance. When an errant shell destroys an ancient stone seal, they find themselves facing a new enemy: hideous NecroMutants, with bone blades that grow from their arms. Mitch barely manages to escape. Nathan does not.

The mutants multiply by millions and they destroy all before them. The Corporation's leader, Constantine (John Malkovich), is about to abandon the planet and leave countless innocents to their desperate fate, when he is approached by Brother Samuel (Ron Perlman), leader of the Brotherhood, and ancient monastic order.

Samuel is keep of the Chronicles, a book that prophesies both the rise of the Mutants, and the 'Deliverer' that will destroy them. Samuel believes he is that Deliverer destined to journey deep into the earth and destroy the source of the mutant scourge.

He manages to recruit Mitch, along with a handful of like-minded soldiers: Steiner, honour bound Bauhaus officer; sword wielding Severian; street fighter El Jesus; fearless beauty Duval; and stoic warrior Juba.

Mutant Chronicles follows Mitch and Samuel's mission to venture into the very heart of the darkness in an attempt to save the planet from marauding hordes of deathless mutants.