The game picks up immediately after the ending of Killzone 2 and follows the previous games' main protagonist, Sev, a Special Forces operative fighting for the Interplanetary Strategic Alliance against the Helghast Empire. The game's story has been referred to being similar to the story of David and Goliath. The game continues shortly after Sev successfully defeated Radec and Rico having killed Visari, the Helghast dictator who leaves them to a fleet of Helghast ships approaching them destroying ISA vessels.
The death of their dictator has left the Helghast Empire in a state of internal struggles with political scheming against each other gripping the Helghast Empire. Now, Sev and his comrade Rico are trapped in the cross-fire between the various political factions in the Helghast Empire without any reinforcements and are left to fight alone in order to escape as the ISA struggles to regroup its forces. The game will also give players a deeper look in to Helghan culture such as their language and showcase whatever humanity they have left within them.
Killzone 3\'s story will also be more light-hearted compared to its predecessor, which Guerrilla felt suffered from an overly serious and dark story which was one of the major complaints of the original, though they mentioned that it would not be too light-hearted as it is still a war. In addition, Guerrilla Games has hired an external writer to focus on only writing the storyline so as to give a fresh perspective to the story as well as hiring a lot more Hollywood actors to elevate the level of storytelling within the dialogue of the game.
Source: Wikipedia, "Killzone 3", available under the CC-BY-SA License.