Starting just after the ending of the original Killzone, and revisiting many of the events from the Killzone trilogy, the game puts players in the rugged combat boots of a mercenary named Arran Danner. Danner, a former UCA soldier, has no qualms about taking on paid contracts from the ISA, as well as the Helghast.
The game starts off during the Helghast invasion on Diortem. Led by Helghast Colonel Vyktor Kratek, the Helghast forces have breached into the Vektan Halls of Justice, in an effort to capture ISA Admiral Alex Grey. It isn't long until the overwhelmed ISA request the aid of the Phantom Talon Corp, an elite group of mercenaries led by Anders Benoit. Shortly after, mercenaries Arran Danner and Damian Ivanov are sent to retrieve the admiral. Danner and Ivanoff make their way to a skyscraper opposite of the building where Grey is being held, and fly down to it in glide suits. They eventually arrive at the Halls of Justice, where Grey is being interrogated. Unfortunately, they are too late. Kratek has already escaped, but not before nearly-fatally shooting Grey. Thankfully, the duo still manage to extract Grey, and the mission is a success.
Fortunately, there is still some work to do in Diortem. After being shot down by ISA forces, a crippled Helghast cruiser lays stranded in the center of the city. On board, a collection of stolen weaponry is being hauled for the trip back to Helghan. Danner and Ivanov are once again requested for the job. After making their way through the cruiser, Danner and Ivanov eventually reach the server room. Here, the two manage to extract transmission codes, which were being used to contact the Helghast fleet. Unfortunately, Ivanov triggers an alarm, causing a quarantine. Ivanov is left for dead, while Danner manages to escape in time. Despite the casualty, the mission is still a success.
Two years later, and the ISA have brought the fight to Helghan. Unfortunately, the invasion is stalled by a collection of Helghast arc cannons. Danner is the sent in, this time with a new mercenary named Carrell. Unfortunately, Carrel is shot down while gliding past the cannons. Nevertheless, Danner still manages to make it to the platform. After infiltrating the station, Danner takes out the arc cannons. After a short firefight, Danner is once again extracted by Benoit, via an intruder.