Russian Ultranationalist leader Imran Zakhaev, who plans to return his motherland to the times of the Soviet Union, draws international attention away from his plans by funding a coup d'tat in an unnamed Middle Eastern country, organized by a local separatist leader named Khaled Al-Asad. Discovering the plot the American government starts a police action to stop the uprising while the SAS continues to operate in Russia. After President Al-Fulani of the Middle Eastern country is executed on live television and Al-Asad takes control, the SAS rescue their compromised informant, Nikolai, from Russian Ultranationalist forces.

One section of the game takes place in Pripyat, Ukraine. Several iconic aspects of the abandoned city, such as this square, were recreated in the game.
During the American invasion of the Middle Eastern country a platoon from the USMC 1st Force Recon, led by Lieutenant Vasquez, searches for Al-Asad but are too late and only secure a television station broadcasting Al-Asad's plan. They then proceed to aid other American units who are fighting a battle against the separatists. During the final stages of the operation United States Central Command learns of Al-Asad's position in the capital but is also notified by SEAL Team Six of a Russian nuclear weapon nearby and sends the Nuclear Emergency Support Team to disarm it. Meanwhile Vazquez's squad is forced to stay behind to rescue the pilot of a downed AH-1 Cobra that was providing them with fire support. They manage to save the pilot. However, the nuclear device suddenly detonates, leveling most of the city, killing most of the US invasion force of 30,000 Marines. While fleeing the city, the squad's helicopter is caught in the blast, killing everyone on board.
The British then learn that Al-Asad fled the country before the American invasion and is hiding in a safe house in Azerbaijan. With the help of Nikolai's intel and assistance from Loyalist Russian soldiers the SAS clear the village of the Ultranationalist forces and capture and interrogate Al-Asad at his safe house. Shortly into interrogation Al-Asad's phone begins to ring. After hearing the voice of the person calling Al-Asad's phone, Captain Price executes Al-Asad, now knowing that Zakhaev is Al-Asad's backer. Price then tells the story of a mission to eliminate Zakhaev in Pripyat, Ukraine, 15 years earlier.
In the aftermath of the Chernobyl disaster and the collapse of the Soviet Union, Zakhaev took advantage of the turmoil to profit from nuclear proliferation and used his new wealth to lure soldiers from the Red Army to form his Ultranationalist Party. In 1996, Price was paired with Captain MacMillan, a Scottish SAS captain, to carry out a black op assassination of Zakhaev. After sneaking into Pripyat and hiding in an abandoned hotel, Price shot Zakhaev with a Barret M82 sniper rifle, but Zakhaev survived, losing his left arm. MacMillan was injured by a crashing helicopter after he and Price shot it down, Price then carried MacMillian to the exfil point.
Back in the present day, a joint operation is conducted by Price's SAS unit, a USMC Force Recon unit led by Staff Sergeant Griggs, and Loyalist Russian forces led by Sergeant Kamarov, to stop Zakhaev. They attempt to capture his son Victor in an unnamed Russian city, to learn of Zakhaev's whereabouts, but as they corner him on the roof of an apartment building, Victor commits suicide to avoid being captured. Zakhaev becomes enraged, blaming Western nations for the death of his son, and plans to retaliate by launching ICBMs armed with nuclear warheads at the East Coast of the United States, with predicted losses of over 41 million people. When the Task Force operatives arrive at the facility in Russia, Zakhaev manages to launch ICBMs towards the United States. However, the squad successfully seizes the silo command room and remote detonates the missiles over the Atlantic. They then escape the facility in military trucks with Zakhaev's forces in hot pursuit.
Before the squad can escape across a nearby bridge it is destroyed by an Mi-24 Hind leaving them trapped. Zakhaev's forces arrive and engage the remaining members of the strike force. Gaz receives a call from Kamarov informing him that his forces are on their way to help. On the bridge a gas tanker behind them explodes, incapacitating everyone, except Griggs, who is killed while trying to pull Soap to safety. Zakhaev, along with two of his soldiers, walks through the squad executing them, killing Gaz and several others. Before he reaches Soap and Price he is distracted by the destruction of his gunship and the arrival of the Loyalist Mi-28 and Mi-8 helicopters. As Zakhaev fires at the loyalist helicopter Price slides his Colt 1911 to Soap who shoots and kills Zakhaev and his two guards. When Sgt. Kamarov and his team arrive Soap is evacuated to safety, while a Russian medic attempts to resuscitate Price.