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During his imprisonment, Mason befriends Viktor Reznov (a returning character from Call of Duty: World at War), a former Red Army soldier. Reznov recounts Mason the identities of those involved in Mason’s torture: Dragovich, Kravchenko, and an ex-Nazi scientist who defected to the Soviet Union, Friedrich Steiner. All three share a connection to Reznov: in October 1945, Reznov, Dragovich, Kravchenko, and Dimitri Petrenko (protagonist of World at War Russia campaign) were a part of a unit sent to locate Steiner. Once Steiner is found, he leads Dragovich to a shipwrecked SS frigate, containing a nerve agent known as "Project Nova". Steiner tells the effects of the gas to Dragovich, but he wants to see first-hand what the gas does. Petrenko and two other Russian soldiers are locked in a room, then gassed while Reznov watches from a window. Reznov is spared when British SAS commandos attack. During the confusion, he destroys Project Nova. It is salvaged by the Russians, becoming known as "Nova-6." Shortly afterward, Reznov is imprisoned in Vorkuta for killing Russian soldiers during the escape from the ship. At Vorkuta, Mason and Reznov spark a prisoner uprising to escape the gulag, but only Mason manages to escape.

One month later, Mason is taken to the Pentagon with his new handler, Hudson. Mason is taken to President John F. Kennedy, who authorizes the assassination of Dragovich. In November 1963, Mason, Woods and Bowman are dispatched to Baikonur Cosmodrome in the Kazakh SSR to disrupt the Soviet space program. Russian-born CIA agent Grigori Weaver is captured during the operation and Kravchenko slices his eye while torturing him (from here on Weaver wears a patch over his eye socket as his eye is lost). The team saves Weaver and eliminate members of the Soviet Ascension program. Dragovich eludes assassination, prompting Mason to search for him over the next five years.

By 1968, the SOG is deployed in Vietnam to investigate the Soviets' presence. After defending Khe Sanh, the SOG is deployed to Huế during the Tet Offensive to recover a dossier with information on Dragovich from a Russian defector. The team recovers the dossier, while Mason encounters Reznov, who is revealed to be the defector. The team later penetrates Laos to recover a Nova-6 shipment from a downed Soviet plane. The mission goes awry and the team is captured. They are taken to a POW camp, and are forced to play Russian Roulette. Bowman, refusing to play, is killed by a Spetsnaz operative while there. Mason and Woods escape, hijack an enemy Hind, and fight their way to Kravchenko's compound. When they arrive, they free the POWs inside, one of which is Reznov. They continue through the facility, finally cornering Kravchenko. When Kravchenko is caught, he arms a grenade in order to kill the rest of the SOG team along with himself. However, Woods tackles him through a window, and only he and Kravchenko are killed. Reznov and Mason then escape and go rogue. Meanwhile, in Hong Kong, Hudson and Weaver interrogate Clarke , an engineer who stabilized Nova-6, in Kowloon. Clarke identifies Steiner as part of the conspiracy, and reveals the location of a hidden facility in Mount Yamantau before being killed by Dragovich's men. Hudson and Weaver head to Mount Yamantau to destroy the facility and apprehend Steiner. During the mission, Hudson receives a transmission from Steiner requesting to meet him at Rebirth in the Aral Sea to learn how to halt a numbers broadcast with instructions to release Nova-6 gas in American cities. Meanwhile, Mason and Reznov head to Rebirth Island to assassinate Steiner. Mason believes he saw Reznov execute Steiner, but Hudson and Weaver witness Mason carrying out the deed. Hudson tackles him to the ground, and uses Mason's Makarov to pistol-whip him in the head, knocking him out cold. Although not seen, he is taken away to be interrogated, beginning the whole cycle of events from the start of the game.

At this point, Hudson and Weaver are revealed as Mason's interrogators. Hudson realizes that Dragovich brainwashed Mason to understand the numbers broadcasts, effectively becoming a Soviet sleeper agent. Out of options, Hudson deliberately sets Mason free in order to follow him. Hudson then reveals to Mason that Reznov was not the defector (the real defector had been killed during the attack on the MACV compound) and that Reznov himself had been killed shortly after Mason escaped Vorkuta. Mason’s visions are of Reznov are shown to be a result of a personality disorder, a byproduct of Reznov having sabotaged Mason’s brainwashing program. Mason was supposed to assassinate Kennedy, but Reznov reprogrammed him to track down and kill the three men responsible for Dimitri Petrenko's betrayal and death. Mason deciphers the numbers, revealing the location of the Russian cargo ship Rusalka off the coast of Cuba.

By dawn, the team launches an assault on the Rusalka, with Mason and Hudson infiltrating an underwater broadcast station protected by the ship, a Soviet submarine station intended to be used as a staging point for US invasion after the planned Nova-6 attack. Confirming that the Rusalka is the numbers station, Hudson calls in theUS Navy to destroy the ship and its underwater base. Mason and Hudson finally kill Dragovich in the lower levels of the station, and swim for the surface during the destruction of the targets, while Reznov's disembodied voice congratulates Mason. Weaver declares victory, but Mason says it is only for now. The story then cuts to a numbers broadcast and then to archive footage of President Kennedy prior to his assassination, with the broadcaster narrating the number sequence and Mason narrating certain numbers and words. Mason's final sayings relate to the assassination of Kennedy, for example, he says "22" which was the day that Kennedy was killed, and "6.5", which was the caliber of the bullet used to kill Kennedy. After a second play-through of the archive footage, Mason’s final words, as well as his presence in the crowd greeting Kennedy's motorcade, suggest that he assassinated Kennedy or that he assisted Oswald in assassinating Kennedy. This theory is supported by Dragovich sarcastically asking "Tried?" before he is killed when Mason says he made him try to kill his President. Note that Kennedy's assassination happens before the events of S.O.G. and after Executive Order, when Mason spends 5 years hunting Dragovich.