Scolar Visari, emperor of Helghan, sends the Helghast Third Army to launch a secret invasion of Vekta. Alerted to the attack, the ISA attempt to prevent it with their SD (Solar Defense) network, but are unable to activate it in time to stop the invaders. With the element of surprise on their side, the Helghast quickly overwhelm the unprepared ISA ground forces and capture several strategic locations, including ISA Central Command.
While taking part in an offensive to slow the Helghast assault, Captain Jan Templar, a veteran ISA officer, is summoned to a meeting by his mentor and close friend, General Bradley Vaughton. Vaughton discloses that the ISA has requested assistance from the UCN and are working to restore the defense network. He also reveals that Colonel Gregor Hakha, a half-Helghan intelligence officer, had, on his orders, infiltrated the inner circle of Third Army commander General Joseph Lente, only to vanish while traveling to an extraction point in Vekta's slums. As Hakha is the only individual with knowledge of how the invasion bypassed SD, he assigns Jan to locate him. After fighting his way through the Helghast occupying the exterior of Central Command, Jan runs into Luger, a former comrade who is now working with an elite ISA division known as the Shadow Marshals. He also recruits the services of Ricardo Velasquez, an ISA gunner seeking revenge for the massacre of his entire platoon.
After rescuing Hakha, the team discovers that General Stuart Adams, the overseer for SD, is secretly working for Lente. He murders Vaughton and takes control of the system, planning to use it to destroy the relief fleet headed to Vekta. Under Jan's leadership, the team destroys several Helghast bases and infrastructure projects, eventually intercepting and killing Lente when he tries to deal with them personally. Adams retreats to the SD control center and tries to reason with the group, explaining that the Helghast will stop at nothing to reclaim Vekta, regardless of how many lives they lose. Nevertheless, the team disables the station and escapes just as the fleet destroys it, killing Adams. Jan and Luger speculate about what the future holds, realizing that the real war is far from over.