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.
The ISA fleet led by Colonel Jan Templar is sent to attack Pyrrhus,the capital city of Helghan,to arrest Visari. Sergeant Tomas "Sev" Sevchenko, a veteran of the ISA battalion joins the Alpha Squad along with Sev's friend,Dante Garza,Shawn Nakto,and Templar's comrade,Ricardo "Rico" Velasquez.
They retrieved a piece of a destroyed tower and sends it to ISA researcher Evelyn Barton, who learns that the towers are powered by Petrusite, a mineral capable of generating and channeling electricity. She also identifies an old mining outpost on the outskirts of Pyrrhus where the Helghast have been secretly extracting it for military use.
Tomas and Rico are separated from the rest of Alpha Squad,who are captured by Colonel Mael Radec and his men. Tomas and Rico manage to reach them. As Radec demands that Evelyn gives him the launch codes to set of stolen nuclear warheads in Helghast Custody. Rico,despite Tomas' orders to stay put,surprises Radec and saves the captives,but getting Garza fatally shot.
The ISA Captain Jason Narville leads the offensive on the the remnants of the Second Army. Radec and his men infiltrated the fleet,killing Evelyn and wounded Jan. The ISA manage to escape with Tomas throwing Radec out of the fleet. Jan maneuvers the ship to crash into the center of Helghan's Petrusite distribution grid before dying, causing it to explode and disrupt the arc network.
The ISA manage to breach the palace where Tomas and Rico confronts Visari,who floats that he has still won. Losing his temper,Rico kills Visari on the spot.
The ISA quickly escape from the Helghan cruisers. As they were about to leave,Radec,who survived,attack the ship. Rico tackles him and the two disappeared through the smoke. Tomas has a feeling that the Armada will not stop.