In October 1944, a group of US commandos infiltrate an island in the Sea of Japan to extract a Japanese scientist with war decisive information. They successfully secure the defecting Japanese scientist who was working on a secret weapon codenamed "The Black Weapon" (a scalar weapon), and attempt to escape the island on a stolen submarine. But after repeated warnings by the scientist, the commandos witness the effects of Black Weapon's power and subsequently perish, sparking a myth about what really happened in Operation Aurora.
In the present day, Bad Company is on a counter-intelligence operation behind enemy lines in Russia in attempt to secure a high value individual of the US military, and a device related to a scalar weapon. Despite escaping Russian soldiers, and completing what they thought was their final mission in B-company, the device is discovered to be a fake. Being impressed with their previous activities, Army General Braidwood assigns them to the Special Activities Division, and tasks them with delivering information to Agent Aguire, much to the disappointment of Sgt. Redford.
The squad travels to Bolivia in search of Aguire. Through many firefights with paramilitaries, they manage to save Aguire just before a Russian hauls him onto a waiting Mi-24 Hind. After discovering that Aguire's findings were stolen by the Russians, Aguire requests the squad to get all his intelligence detailing the scalar weapon from a satellite. The squad moves up to take the mountain with assistance from their pilot Flynn and his UH-60 Black Hawk. After taking over the satellite station, Sweetwater codes the satellite to crash, with the squad driving over cross country to find it, taking on Vodniks and Quad Bikes along the way. After reaching the satellite, the squad successfully defeat a Russian counterattack aimed at destroying the satellite, but soon bad weather rolls in. While Redford and Haggard go to find transport, with Sweetwater following, Marlowe soon finds the data storage unit and proceeds to go down the mountain during a blizzard, taking on Russian patrols, and is soon extracted by the others in Flynn's helicopter.
During extraction, Aguire briefs the squad about the man responsible for building a scalar weapon named Arkady Kirilenko; the Russian Army colonel the squad failed to eliminate in Chukotka, who is believed to be hiding in Chile. Marlowe and the squad travel to Chile, where they, aided by US Armoured forces and Marines, find Kirilenko, though he soon escapes after US Command starts shelling Kirilenko's position. Left only with papers from Kirilenko's office, Sweetwater discovers there is a shipping manifest for a lost ship called the "Sangre del Toro." Aided by the rest of the squad getting the coordinates, Marlowe finds the ship and retrieves an unnamed compound essential to the use of the weapon, and finds out the truth behind Operation Aurora.
While attempting to meet Aguire in Colombia, the squad's helicopter is shot down by a Javelin and they become separated. Sweetwater and Marlowe regroup first, taking on a militia counter-attack, and they soon find the rest of the squad. After fighting through heavily defended Russian bases, the squad find Flynn, and then race to a helicopter base on Quad Bikes. After fighting through Russian territories in a salvaged Black Hawk, the squad reach the rendezvous with Aguire, and Marlowe gives Aguire the compound, while Redford demands to know what's happening. However, Aguire double-crossed the squad by allying with Kirilenko, his rival in the quest for the scalar weapon. Aguire wanted revenge against the United States for what happened to his father, one of the commandos in original raid on Japan, after Marlowe revealed that the US military callously sent them to their deaths. Despite the alliance, Kirilenko betrays Aguire and kills him. Flynn intervenes and saves the squad at the cost of his own life, his helicopter shot down by an RPG.
While still mourning after Flynn's loss, the squad overhear a Russian soldier's radio, which the squad use to find their position. They begin to move towards a city, but then Kirlienko begins the detonation of the scalar weapon. The squad begin advancing through a Venezuelan city, being attacked by Russian and militia troops, along with mortars. However, as they reach the mouth of a large river, they witness a huge firefight between US and Russian troops. However, as the fight reaches a climax, the scalar weapon detonates, annihilating the US forces and sending "all tech dead." The squad then fight through the blast zone in pursuit of Kirilenko, but, as the squad reach the plane, an An-124 Ruslan (Which Haggard mistakenly identifies as an An-225 Mriya), they realize it's taking off. The squad unanimously vote that they should hijack the plane, and set off through sewer tunnels towards it. Though they had to discard their weapons, they climb on board through the undercarriage, and await dawn.
The squad begins to progress through the plane, taking out multiple guards before reaching the scalar weapon, which is protected by a reinforced pane of glass, which Haggard says will "take an act of God to get through, or a lot of C4." The squad then fight towards the cockpit of the plane, but realize that Kirilenko is in the Scalar chamber itself when they discover that the cockpit is empty. After detonating C4 to get through the glass, the squad destroy the Scalar weapon, and then proceed to bail out of the plane. However, as Sweetwater tries to give Marlowe the last parachute, Kirilenko tackles him, and Marlowe is forced to dive out of the plane, killing Kirilenko in a free fall with an MP-443. Sweetwater passes Marlowe a parachute in midair, and the pair land safely in Texas alongside the rest of the squad. However, as they begin to celebrate, General Braidwood tells them to follow him in a HMMVW, as the Russians are invading through Alaska.
The last cutscene shows a map of Russian forces swarming through Alaska and Canada, quickly advancing on the US border.