On February 25, 1968, SOG operative Alex Mason is strapped to a chair in an interrogation room, bombarded with questions by his unseen captors about the location of a numbers station. Mason then recalls several events, as an attempt to answer their questions.
In 1961, Mason, Woods, and Bowman take part in Operation 40 to assassinate Fidel Castro in Cuba during the Bay of Pigs. Mason apparently succeeds and stays behind to protect the extraction plane from an oncoming blocade, before being captured by the real Castro, having shot a double. Handed over to General Nikita Dragovich to be held captive at Vorkuta Gulag, Mason befriends inmate Viktor Reznov, the former Red Army soldier. Reznov recounts to Mason the identities of his enemies, the same people involved in Mason’s torture: Nikita Dragovich, his right-hand man Lev Kravchenko, and ex-Nazi scientist Friedrich Steiner, who defected to the Soviet Union.
In October 1945, Reznov and Dimitri Petrenko were sent to extract Steiner from a Nazi base in the Artic. Dragovich later betrayed them by testing Steiner's creation, a nerve agent known as "Nova-6", on Petrenko and other soldiers in a ship. Reznov was spared the same fate when British commandos, also attempting to acquire Nova-6, attacked the Soviets. During the confusion, Reznov destroyed the Nova-6 and escaped. However, the Soviets recreated it using Steiner and a British scientist, Daniel Clarke. Mason and Reznov later spark a prisoner uprising to escape the gulag, but only Mason escapes and Reznov is captured. One month later, President John F. Kennedy meets Mason and authorizes a mission to assassinate Dragovich. Mason briefly envisions aiming his side arm at Kennedy.
In November 1963, Mason, Woods, Bowman and Weaver are dispatched to Baikonur Cosmodrome,kh SSR to disrupt the Soviet space program and eliminate members of "Ascension", a Soviet program giving sanctuary to Nazi scientists in exchange for their knowledge. Weaver is captured and Kravchenko stabs out his left eye. Mason and his team rescue him and destroy the Soyuz spacecraft, while Woods apparently kills Dragovich, though Mason believes him to be alive.
In 1968, the team is sent to Vietnam. After defending Khe Sanh, they recover a dossier on Dragovich from a Russian defector in Hue during the Tet Offensive. Mason finds the defector is none other than Reznov. They then penetrate Laos to recover a Nova-6 shipment from a downed Soviet plane. At the crash site the plane collapses and they are captured by Viet Cong and Spetznaz infiltrators. Bowman is executed, while Woods and Mason hijack an Mi-24 Hind and rescue Reznov at Kravchenko's base before confronting Kravchenko himself. Woods stabs Kravchenko, gaining the upper hand. But then as Kravchenko pulls the pins off four grenades strapped to his chest, Woods sacrifices himself by pushing Kravchenko and himself out a window. In a huge explosion, Mason presumes the two dead.
Meanwhile, Hudson and Weaver interrogate Clarke in Kowloon. Clarke reveals the location of a hidden facility in Mount Yamantau before being killed by Dragovich's men. Hudson and Weaver move to destroy the facility and receive a transmission from Steiner requesting to meet at Rebirth Island, as Dragovich has begun killing loose ends. Mason and Reznov head there to assassinate Steiner at the same time, succeeding just as Hudson and Weaver arrive. Mason is adamant that Reznov executed Steiner, but Hudson had witnessed Mason carrying out the act alone.
At this point, Hudson and Weaver are revealed as Mason's interrogators. Dragovich has communist sleeper cells placed all over the United States which, when ordered by the numbers broadcast, will release the Nova-6 gas. As a result, the U.S. is preparing a retaliatory strike on the Soviet Union, which will lead to a full scale war. Hudson needed Steiner to abort the gas launch but after his death only Mason has any knowledge of the numbers station. Hudson reveals that Dragovich brainwashed Mason to understand the numbers broadcasts, effectively making him a Soviet sleeper agent. It is revealed that the real Reznov never escaped and died during the Vorkuta break out, and that the Soviet defector in Hue was actually killed before Mason reached him. Mason’s visions of Reznov are a result of a dissociative order caused by the traumatic brainwashing program. Prior to the Vorkuta breakout, Reznov had secretly met and reprogrammed Mason to assassinate Dragovich, Kravchenko and Steiner for what they did to him and for killing Petrenko and his comrades, instead of Mason's original aim to kill the U.S. President. Mason finally remembers the location of the station: a Russian cargo ship called Rusalka off the coast of Cuba.
An assault on the Rusalka begins, with Mason and Hudson infiltrating the underwater submarine and broadcast station protected by the ship, intended to be used for an invasion of the U.S. after the planned Nova-6 attack. Confirming that the Rusalka is the numbers station, Hudson calls in the US Navy to destroy the ship and its underwater base. Mason and Hudson finally confront Dragovich in the lower levels of the facility. Dragovich taunts Mason and hints at his hand in assassinating Kennedy but Mason drowns him and escapes.
Archive footage of President Kennedy prior to his assassination is shown, revealing Mason in the crowd, implicitly suggesting that Mason may have carried out his initial programing.
In 2025, US Special Forces operatives led by David Mason and his partner, Harper, arrive at "the Vault", a top-security location home to an elderly Frank Woods, whom they suspect possess vital information on the whereabouts of Raul Menendez. Woods concedes that Menendez has recently visited him, and shows them a locket that the latter had left behind. Frank then narrates several covert missions undertaken during his military career which span their previous encounters.
1980s
In 1986 Alex Mason had effectively retired from active duty to pursue an obscure existence in Alaska with his son, the seven-year-old David. Their shaky relationship is further strained when Mason is solicited by Jason Hudson, seeking to recruit him for an assignment in Cuando Cubango during the height of the Angolan civil and South African Border Wars. Woods had disappeared with his men while aiding Jonas Savimbi's UNITA rebels against Angola's Marxist government; their actions have already been disavowed by the CIA and Hudson hopes to rescue any survivors. With UNITA assistance, Mason and Hudson recover Woods from the Kavango River, subsequently locating Menendez among a contingent of Cuban military advisers. However, a firefight breaks out, and their quarry escapes as the Americans are rescued by Savimbi in a Hind D. It is revealed that Menendez is responsible for holding Woods captive after murdering his team.
In light of this information, Mason, Woods, and Hudson begin tracking Menendez, who has established himself as a primary arms dealer for bush conflicts in Southern Africa and Latin America. Later in the year, the CIA authorizes a strike against the unscrupulous Nicaraguan, now making a healthy profit running arms across Soviet-occupied Afghanistan. In Afghanistan, Mason, Woods, and Hudson assist the Mujahideen in their battle against the Russians, along with Chinese operative Tian Zhao. Woods and Mason find Lev Kravchenko, who had survived the grenade incident with Woods in Vietnam, causing Mason to see the numbers and hear the voice of Viktor Reznov again.
Kravchenko is interrogated by the group and the player is given the option of executing Kravchenko by Reznov's orders inside Mason's head or resisting and finishing the interrogation, in which case, Woods then executes Kravchenko after admitting that he associated with Menendez and that he has men inside the CIA. Regardless of how Kravchenko is killed, the Mujahideen are revealed to be allied with Menendez, and double-cross Mason, Woods, Hudson, and Zhao. The four are beaten, tied, and left for dead in the middle of the desert, unconscious until rescued by two unknown civilians, one of whom Mason believed to be Reznov.
At this point, Menendez's motive for his seemingly senseless vendetta against the West become clear: his beloved sister was grievously injured in an act of arson committed by American businessmen for insurance money. The Menendez clan, which dominates a powerful drug cartel, was again rocked by loss when the CIA sanctioned the assassination of Raul's father. An embittered Menendez now considers the conflict to be personal, but his one-man struggle against the West is interrupted when Mason, Woods, Hudson, and the Panama Defense Force raid his headquarters in Nicaragua; an enraged Woods inadvertently kills Raul's sister with a grenade.
Faking his demise with the assistance of Panamanian dictator Manuel Noriega, Menendez lives to retaliate against those he holds personally responsible for his sister's death. During the 1989 invasion of Panama, he utilizes moles in the CIA to kidnap Hudson and Alex, using them as bait for a trap. He then uses Hudson to mislead Woods, manipulating him into shooting Mason instead of himself. If the player disobeys Hudson's instructions to shoot Alex Mason in the head and instead shoots him anywhere else, he will survive and reappear in the game's ending. In the ensuing chaos, Menendez kills Hudson and cripples Woods. Unsatisfied with his revenge, Menendez allows Woods and David to live, promising to return to complete his revenge when the time is right.
2025
36 years after Panama, Menendez re-emerges as the leader of Cordis Die, a massive populist movement with over a billion followers. He stages a cyberattack that cripples the Chinese Stock Exchange; in response, the Chinese government bans the export of rare earth elements which the entire infrastructure of the US Army runs and relies on, formenting the start of the Second Cold War between the United States and NATO, against the Chinese-led SDC (Strategic Defense Coalition). Taking advantage of this stand-off, Menendez attempts to bring the two superpowers to a full-blown war by inciting conflicts between the two, secretly aiding SDC leader Chairman Tian Zhao. Using the intelligence provided by Woods, David, now a Navy SEAL code-named Section, leads JSOC units in the search for Menendez.
Shortly after gathering intelligence from Woods, Section and JSOC infiltrates Myanmar investigating suspicious activities in the region. There, Section's team encounters a computer engineer under Menendez's employment, warning them of a cyberattack with a Celerium device, a quantum computer capable of hacking any computer system. Section's team is later deployed in Pakistan, attempting to gather intelligence on Menendez's plots. During the infiltration, Menendez discloses the name of a target, "Karma" in the Cayman Islands. Section and SEAL operatives Harper and Salazar later infiltrate the Cayman Islands, finding out that "Karma" is a woman named Chloe Lynch, a former employee of Menendez's shell corporation, Tacitus. Lynch was the main developer of the Celerium device, and as a means of wrapping up loose ends, Menendez had deployed mercenaries for her abduction.
JSOC later has a lead on Menendez in Yemen, where JSOC asset Farid infiltrates Menendez's cell to help Section facilitate the leader's capture. The player, as Farid has a choice during the mission. Menendez, suspecting Farid's disloyalty, orders him to shoot the captured Harper. If the player chooses not to shoot Harper, and instead attempts to shoot Menendez, he fails, but Harper survives and is rescued. If the player chooses to shoot Harper, Farid survives, and Harper is not present in any conversations or missions thereafter. Menendez is successfully captured, but this was a ruse for Menendez to hack into the U.S. military's computer infrastructure on the aircraft carrier Barack Obama, seizing control of the United States' entire drone fleet. Salazar is revealed to be Menendez's mole within JSOC, and facilitates Menendez's attack—Menendez escapes with Salazar's aid, and when Menendez breaks in to the bridge of the Obama, Salazar shoots the soldiers guarding Admiral Briggs, with Lynch's survival dependent on Farid's survival in the previous mission.
The player, playing as Menendez, has the choice of either killing or wounding Admiral Briggs. If the player only wounds Briggs, and the player has completed all of the Strike Force missions, JSOC and SDC enter an alliance, then the player is later informed that the SDC sent hundreds of drones to defend the Obama, and consequently Briggs was able to save the ship and its crew. Menendez hacks into the military satellite to gain access to the entire U.S. drone fleet to stage an attack on Los Angeles during a meeting of G20 leaders, hoping to kill them and cause catastrophic damage to the global economy and to attack several targeted cites in America and China to cripple their infrastructure. Section escorts the President of the United States to safety amidst the drone attacks.
JSOC eventually traces the source of the transmissions responsible for the hacking to Haiti, where Section leads JSOC forces into recapturing the facility in the final mission, and apprehending or killing Menendez. There are different endings depending on the actions the player takes throughout the campaign, such as whether or not the United States and China are able to enter an alliance with each other, as well as determining the fates of certain individuals in the game.
During the main campaign, the player may choose to participate in optional Strike Missions. The Strike Missions involve JSOC attempting to curb the SDC's global influence by preventing them from forcing neighboring countries into the alliance. Section himself does not participate in these missions directly, though he can command the forces remotely from a command center. If the missions are completed successfully, the SDC is weakened enough to ally with JSOC, forming an alliance between the United States and China, with the Chinese assisting the player later in the campaign, for example, in sending its own drones to rescue the U.S.S. Obama and sending its forces to assist JSOC in Haiti.
