The game is set in an era of space colonization where the Helghast Empire has recovered from its defeat in the First Helghan War and launched a blitzkrieg against the outer ISA colony planet Vekta. Vekta’s orbital Strategic Defense (SD) platforms failed during the initial assault, allowing the Helghast to land swarms of soldiers onto the surface. This makes it all the more difficult for the outnumbered ISA forces.

In the game, the Helghast are a faction of human descendants who colonized the planet Helghan many generations ago. The planet’s harsh environment forced the Helghast to adapt and mutate so much that they can no longer be considered human. They are stronger, faster and more resilient than their cousins, and possess a burning hatred for humanity. Except for a small number of half-breed Helghast and trained troopers, they require a gas mask and air tank with air similar to the planet Helghan’s atmosphere. Vekta’s only hope rests with an elite squad of four soldiers who will become heroes.

The player takes control of ISA squad leader Jan Templar, fighting off the Helghast invasion. Templar and his squad are called back to the base for reassignment, and are promptly sent to find the ISA operative Hakha and the key in his possession. During the course of the game, the player also takes control of several other characters, such as a special operations agent Luger (a female "Shadow Marshal" assassin), a heavy weapons specialist sergeant Rico Velasquez (a Helghast-hating grunt from the slums with an itchy trigger finger), and Hakha, a half-Helghast, half-Human spy.