The game begins in October 1944, as a group of US commandos infiltrate an Imperial Japanese Navy-controlled island in the Sea of Japan as part of “Operation Aurora.” They secure a Japanese scientist who was working on a secret scalar weapon, and escape the island on a submarine. However, as foreshadowed by the scientist’s warnings, the commandos witness the weapon firing and subsequently perish from the resulting tsunami, sparking a myth within the U.S. Army.
In the present day, Privates Preston Marlowe, Terrence Sweetwater, George Haggard and Sergeant Samuel Redford are fighting in Russia in an attempt to secure a scalar weapon device. Despite evading Russian soldiers and completing the mission successfully, the device is discovered to be a fake. Impressed with their previous activities, Army General Braidwood has the squad transferred into the Special Activities Division and assigns them a new mission; to contact Agent James Wyatt (called Aguire in-game), much to the disappointment of Redford, who had hoped to retire after the previous mission.
The squad travels to Bolivia in search of the agent, and after many firefights, they eventually save Aguire. He sends them to retrieve his scalar technology intelligence from a French weather satellite that can be controlled from a base in the Andes. Sweetwater lands the satellite and the squad successfully defeat a Russian attempt to destroy it. Marlowe locates the data server and proceeds to descend the mountain during a blizzard while dodging Russian patrols. He survives, and is extracted by the others.
During extraction, Aguire briefs the squad about the man responsible for rebuilding scalar weaponry; Arkady Kirilenko, a Russian Army colonel the squad encountered in Russia. Kirilenko is hoping to use scalar weaponry to disable America’s power grid and pave the way for a Russian invasion. He is believed to be hiding in Chile. The squad head there, aided by US forces, and find Kirilenko, who escapes again. Left with only Kirilenko’s papers, Sweetwater discovers there is a shipping manifest for an abandoned ship called the Sangre Del Toro. Aided by the rest of the squad, Marlowe finds the ship and retrieves a compound essential to the use of the weapon, while also discovering the truth behind Operation Aurora – the US military knew it was a suicide mission, and the operation was planned in order to learn more about the weapon’s capabilities.
While attempting to meet Aguire in Ecuador, the squad’s helicopter is shot down and they are separated. Along with their helicopter pilot, Flynn (Eric Loren), they regroup and escape the local militia. Redford gives Aguire the compound before finding out that Aguire has double-crossed them by allying himself with Kirilenko. Aguire reveals that he wants revenge against the United States for what happened to his father, Thomas Wyatt (the leader of the commandos killed in 1944 during Operation Aurora). Despite this, Kirilenko betrays Aguire and kills him. Before he can kill the squad, however, Flynn intervenes and saves them at the cost of his own life.
While the squad is mourning Flynn, they hear Kirilenko talking through a guard’s radio. Marlowe knifes the guard and the squad proceeds toward the city of Quito. Here, after battling squads of South American and Russian troops, they find a large cargo aircraft that is believed to house the scalar weapon. This is confirmed as a powerful electromagnetic pulse is suddenly released, disabling all electronic equipment in the city except the aircraft. Haggard and Sweetwater become disheartened, with Haggard going so far as suggesting the squad abort the mission. Angry at his allies for giving up, Marlowe is about to continue the mission alone before Redford stops him and then convinces the rest to continue. They then infiltrate the aircraft as it takes off. After a firefight to reach the cockpit, they find it empty. They return to the cargo bay to find Kirilenko attempting to fire the scalar weapon again, this time high over the southern United States. With the help of explosives from the plane’s armory, they access and destroy the scalar weapon.
The explosion sends the aircraft plummeting, forcing the squad to bail out, but Kirilenko grabs the last parachute before Marlowe. In free fall, Marlowe kills Kirilenko, and is then saved by Sweetwater who hands Marlowe the parachute that was stolen by Kirilenko. The squad lands in Texas, Haggard’s home state. Shortly after, General Braidwood arrives to inform them that they are to aid the US Army against an incoming Russian invasion that recently passed through Alaska and Canada, much to the squad’s disappointment.