Back story:

We've colonized other planets, and the Helghan corporation colonized Helghast. Due to the planets natural gasses, futher generations pigmentation changed all up, and the working class, who mined the planet, began wearing respirators. Soon enough, their eyes turned red so they could see better in all the dust, and the people grew restless, blaming the other worlds because they got the short end of the stick and refuse to ship out any resources. A war erupts, brutal, long, but the Vektans and ISA emerge victorious over the Helghans.

A few years pass, and Scolar Visari rises to power on Helghan, renames their infantry as 'the Helghast', and promotes the use of the gas-masks to not only instill fear in their opponents, but to keep his soldiers breathing the poisoned air on other planets during invasions, as straight oxygen makes the sluggish. He sends troops to invade Vekta, which has a large satellite defense grid, which suspiciously fails during the initial assault on the planet. There is a traitor general (killed in KZ1 by Jan and Rico). Jan, the commander of The New Dawn, the dropship you're on, is the hero of the first game and Killzone Liberation. After repelling the Helghast invasion, a few of their nukes are stolen by a commander and General Radec, but they failed to acquire the launch codes.

Trying to put an end to the war, the ISA/Vektan forces invade Helghan, assuming when they capture Scolar Visari, that the Helghan forces moral will drop to the point of surrender.

That's the basic plot.