Killzone 2 spoilers
In the prologue, the ISA has set up their Cruiser airships, including the New Sun, up in the clouds of Helghan over its capital city, Pyrrhus, preparing for a final attack. Then, the invasion begins. The ISA, including Alpha Team, are deployed in an attempt to capture the city. The invasion is seemingly successful until the Helghast activate their main defense system, a series of arc towers throughout the city, killing many soldiers and severely damaging the first wave of the assault; however, the fight between the ISA and Helghast continues.
Using a piece of an arc tower picked up earlier, scientist Evelyn Batton discovers that the arc towers are composed of an element called Petrusite, and large portions of the mysterious element are located around the outskirts of Tharsis Refinery. The Alpha team is ordered to accompany Evelyn and travel to the outskirts of the city in an attempt to find a way to disable the towers.
During the mission, Sev and Rico departs from the others in order to activate a communications tower. Before the tower is activated, however, Garza, Natko and Evelyn are captured by Helghast. Eventually, Sev and Rico find their squad: they see Colonel Radec and his guards preparing to execute them. While Sev waits, Rico's impatience causes him to rush in, in an attempt to save the squad. Unfortunately, Garza is mortally wounded and Radec escapes. The only thing they can do is return back to the New Sun. Evelyn heads to the nearest Communications tower to call for extraction. The squad is then attacked by more Helghast troops, but they are able to fend off the enemies. Unfortunately, when ISA support finally lands, Garza collapses and dies in Sev's arms.
Back aboard the New Sun, Sev mourns for Garza; however, it is interrupted by a Helghast attack on the ISA fleet. All ships, including the New Sun, are invaded. In the assault, Colonel Radec reaches the bridge where he kills Evelyn and Fleet Commander, Colonel Jan Templar. Before leaving, Radec steals the nuclear strike codes for the (previously stolen) nuclear weapons. Templar, left to die on the bridge, manages to deactivate the thrusters on the New Sun, sending it falling down to Helghan. Luckily, the ship crashes into Tharsis Refinery, destroying the city's petrusite defense grid.
With the grid down, the ISA advance and attempt to regroup near Visari's palace in Pyrrhus; however, a nuclear bomb is detonated within the city, destroying the city, along with most of the ISA forces. Despite such events, Alpha team and the last remaining ISA attack the palace amidst very heavy casualties.
During the final assault, Sev and Rico severely injure Radec, who chooses to commit suicide to avoid capture.
Finally, Sev and Rico find Scolar Visari who is waiting for them. He tells Sev that the war is far from over, and if they capture or kill him, the Helghast would remember him as a martyr. This would cause the Helghast to fight with more determination in order to destroy the Vektans, and that he is the only one who is keeping the Helghast "under control".
Rico, who decides to avenge Templar along with other ISA members, shoots Visari. As Visari succumbs to his injuries, he mutters his last words: "The Madness Begins."
Worn from all the occurrences, Sev leaves the palace and sits on the entrance stairs. There, he sees an overwhelmingly giant Helghast fleet destroying what is left of the ISA fleet and sees, first hand, what Visari envisioned.