Campaign

In January 1981, CIA SAD/SOG operatives Russell Adler, Alex Mason, and Frank Woods are sent to target Qasim Javadi and Arash Kadivar for their roles in the Iran hostage crisis. With intelligence gained from interrogating Qasim, the team tracks Arash to Turkey, where the three witness him executing everyone in the vehicle he arrived in. Arash boasts that Perseus was the one responsible for organizing the hostage crisis before being executed. US President Ronald Reagan authorizes a black operation team to neutralize Perseus after being briefed of his threat by Jason Hudson and Adler.

Adler's team consists of CIA operative Lawrence Sims, American born Mossad operative Eleazar "Lazar" Azoulay, and MI6 intelligence officer Helen Park, with Mason and Woods providing tactical support. The final member of the team is an agent known only by the codename "Bell", who served with Adler and Sims in MACV-SOG during the Vietnam War. The team starts by asking Bell to recall Operation Fracture Jaw in 1968, where Adler believes he, Bell, and Sims first encountered Perseus. Afterwards, the team proceeds to East Berlin to apprehend/kill Anton Volkov, a Russian mafia boss with ties to Perseus.

Following an infiltration into a secret Spetsnaz training facility by Bell and Woods, the team discovers that Perseus had infiltrated Operation Greenlight, a top secret American program that secretly planted neutron bombs in every major European city to deny their use to the Soviets in the event of an invasion. Mason and Woods are deployed to Mount Yamantau in the Ural Mountains, where they infiltrate Nikita Dragovich's destroyed base in hopes of retrieving his list of sleeper agents.^{[lower-alpha 3]} However, the team finds out that Perseus has wiped the data from the Yamantau base's mainframe, leaving their only option to infiltrate KGB Headquarters to retrieve the list. Enlisting the help of one of their KGB double agent allies, Dimitri Belikov, they manage to get Adler and Bell inside the Lubyanka Building. The team learns that an Operation Greenlight scientist is one of the sleeper agents and has fled to Cuba. Hoping to catch Perseus there, the team launches a raid. They learn that Perseus has managed to steal the detonation codes for every Operation Greenlight bomb, meaning he can devastate Europe and lay the blame on the United States. The team comes under heavy fire and Lazar and Park are injured in the process, leaving Bell only enough time to save one of them.

After rescuing Bell, Adler continues to press them by provoking their memories of Vietnam once more. At this point, Bell's true identity is revealed as an agent of Perseus, having been shot by Arash in Turkey out of jealousy. Bell was found by Adler and was brainwashed using Project MKUltra into believing they were his comrade. With Bell's memory returned, Adler interrogates them on the location of Perseus' headquarters. Bell can then either choose to remain loyal to Perseus and lie to Adler, or choose to betray Perseus and reveal his location.

• In the non-canonical endings where Bell chooses to stay loyal to Perseus, they lie by telling Adler to head to the Duga radar array, where the team will be too far away to stop Perseus from activating the nukes. If Bell has established contact with the Soviet Army beforehand, they will lure the team into a trap and kill them with the help of Perseus and the Soviet Army before they activate the nukes. If Bell refuses to kill the team, Bell is executed by Adler but the nukes will still go off. Europe is devastated by the explosions and public opinion of the United States plummets. The CIA is forced to erase the existence of Adler and his team in an effort to cover up the United States' involvement in Operation Greenlight. Perseus boasts that his agents in Europe will take advantage of the chaos to infiltrate every European government and turn them towards the Soviet Union, while his agents in the United States will continue to undermine the country.
• In the canonical ending where Bell decides to betray Perseus and help the CIA, they along with the team assault Perseus' headquarters in the Solovetsky Islands and destroy the transmitters needed to send the detonation signal. With the failure of Operation Greenlight, Perseus goes into hiding, though Adler swears to continue pursuing him and dismantle his spy network. Later, Adler takes Bell out for a private conversation, assuring them that their choice to turn against Perseus was of their own free will and that they are a hero. Adler then admits that Bell must be eliminated as a loose end and both draw their guns, with the scene fading to black as gunshots are heard.

Multiplayer/Warzone

Two years after Operation Greenlight's failure, a Perseus cell infiltrates the Cheyenne Mountain Complex and successfully hijacks a nuclear ICBM during military exercise Able Archer 83. Operators from NATO and Warsaw Pact countries are deployed to various hot zones, where Perseus activities are sighted. On January 20, 1984, a Perseus cell, led by Vikhor "Stitch" Kuzmin, raids a CIA safe house in West Berlin in order to gain intel on Adler. Stitch, who was in charge of Nova-6 production on Rebirth Island, vowed vengeance on Adler, who captured and tortured him during the CIA's assault on the island in 1968. Stitch leaves behind a message to taunt Adler that leads him to a mall in New Jersey. At the mall, Adler's team runs into an ambush by Stitch, who has also set up a cache of Nova-6. The team attempts to escape, but Adler is ultimately captured and taken away by Stitch and his men.

Three months later, Woods leads a squad to Laos where Adler was last sighted, only to learn that he has been transported to Verdansk. Hudson authorizes a search and rescue operation to retrieve Adler. On June 2, 1984, two Perseus operatives, Freya "Wraith" Helvig and Roman "Knight" Gray, infiltrate the Yamantau secret military base and retrieve data related to Dragovich's numbers program, which Stitch plans to use in order to create more sleeper agents across the nation. They then detonate the base, intending to shift the blame toward the U.S. and spark another war. Eight days later, Woods manages to locate Adler in Verdansk and rescue him.

Some times later, Stitch orders Perseus operative Owethu "Jackal" Mabuza to assault Jumpseat Satellite Ground Station in South Africa. The station's surviving specialist is forced to obey Stitch's order as he de-orbits two CIA satellites, which end up crashing in Verdansk and Algeria, respectively. Following his recovery, Adler immediately leads a squad to investigate the satellite crash in Algeria. As they approach the crash site, Adler recklessly charges in and eliminates Perseus agents, while secretly recovering a data recorder from the satellite debris. A month later, Woods leads a response team, accompanied by Colton "Stryker" Greenfield, to the ECHELON Listening Station in Teufelsburg, where they attempt to apprehend Perseus operative Kaori "Kitsune" Tanaka. Kitsune, who has just finished uploading the numbers protocol, activates the sequence, turning the response team against Woods and Stryker, who narrowly escape death. Afterwards, Hudson meets with Woods in private and reveals an inconsistency in Adler's statement about the data recorder from the Algeria satellite crash site, as well as his recent unmonitored activities in Verdansk. Recognizing that Adler may have been compromised due to the numbers program, Hudson orders Woods to contact Mason for help.

On August 2, 1984, Stitch and Perseus operative Benito "Fuze" Ortega attempt to defuse several explosive charges planted all across Verdansk by Adler. Meanwhile, Adler is put through extensive torture by Mason and Hudson in order to break his programming. Mason succeeds in deprogramming Adler, while Stitch's team fails to stop most of the charges from detonating. Woods, Adler, Mason and Hudson are deployed at a heavily destroyed Verdansk to confront Stitch for the final time. They eventually find Stitch in the woods, where Adler learns that he had taken over the mantle of Perseus, while the previous one passed away from cancer in 1983. Having finished his work, Stitch willingly surrenders his life, while taunting Adler of his actions. A gunshot is heard as the scene cuts to black.

A few days after, Adler, Mason, Woods and Hudson investigate an underground Nazi bunker in the ruins of Verdansk, where they meet Captain Carver Butcher, a retired Special Operations Executive agent and founder of Task Force Vanguard. Butcher begins telling Adler and the others of his mission in leading various special operations task forces to hunt down remnants of the Nazi empire in the Pacific.^{[lower-alpha 4]}

Zombies

In 1983, CIA Special Officer Grigori Weaver is contacted by an acquaintance, former BND operative Samantha Maxis,^{[lower-alpha 5]} who provides him with secret KGB intelligence. Weaver learns from Maxis that during World War II, the Nazis attempted an experiment in a secret bunker in Morasko, Poland where they managed to reanimate dead soldiers into zombies. Afterwards, the bunker was discovered and sealed by the Soviet Union, only to be recently uncovered by Omega Group, a KGB-Spetsnaz joint research team working in favor of the Soviet Union. As a result, several Dark Aether anomalies begin to appear around the world, unleashing zombies in their wake. A classified task force codenamed Requiem is assembled to combat the global undead threats as well as conduct research into the anomalies for technological advancement.

In November 1983, Requiem deploys a strike team to the bunker in Morasko, dubbed Projekt Endstation, where they discover a rift that acts as a gateway to the Dark Aether dimension, responsible for other global dimensional breaches. Upon further investigation, the strike team uncovers a device in the facility called Der Wechsler, which can restore a zombie's brain functionality. The strike team uses it on one of the roaming zombies in the facility, who was a former Omega Group member named Orlov. In turn, he agrees to help the team close the dimensional rift. Orlov successfully seals the rift, destroying Endstation and sacrificing himself in the process, while allowing the strike team to escape.

Following Endstation's destruction, Maxis investigates further into Omega Group's activities, and travels to Outpost 25, located in A Sầu Valley, Vietnam, but is captured by Omega forces and thrown into the Dark Aether dimension. In June 1984, the Requiem strike team arrives at Outpost 25, and makes contact with Captain Sergei Ravenov, Maxis' mole within Omega. Ravenov guides the strike team through the undead-infested facility, while also dealing with Doctor William Peck, an American scientist who defected to Omega. After learning from Peck of Maxis' current situation, the strike team attempts to open a portal and stabilize it long enough for Maxis to escape the dimension. They eventually succeed and exfiltrate with Maxis, while Ravenov elects to remain undercover as Omega continues their operations in the Ural Mountains. Following Requiem's success, Omega's leaders, Colonel Lev Kravchenko and Doctor Aleksandra Valentina, travel to Outpost 25 to confront Peck about his failure.

In an effort to catch up to Omega Group's progress, Requiem launches Operation Threshold, a large-scale mission across the Ural Mountains where the largest outbreak zones have been identified. Over the next several months, Requiem operators are deployed in multiple Ural regions in order to eliminate undead targets, capture specimen and commence further research on the mysterious Aetherium element. Meanwhile, Maxis is quarantined under isolation due to her time spent inside the Dark Aether dimension. In November 1984, Maxis secretly contacts the Requiem strike team during their mission, requesting them to meet with Ravenov. At the missile silo in Ruka, Ravenov reveals that Peck has been using Aetherium crystals to supercharge nuclear warheads, which would allow Omega Group to create new outbreak zones wherever they choose. Not wishing to let either side possess the warheads, Maxis instructs Ravenov and the strike team to work together and direct the warheads toward the Pacific Ocean where they can be safely dumped. After clearing out a massive zombie horde guarding the silo, the strike team succeeds in deploying the warheads and manages to exfil.

Afterwards, Ravenov contacts Weaver via Maxis' secret radio channel, and requests Requiem's help in extracting several Omega scientists who wish to defect from the group. Though angry at Ravenov and Maxis' secrecy, Weaver agrees to help him carry out the operation. Some times later, the strike team receives intel from Ravenov that he has lost contact with the scientists. The team is sent to the State Sanatorium U-23 to investigate a crash site and help extract the scientists; however, they were all murdered by Doctor Hugo Jager, an Omega scientist who was secretly a mole planted by Kravchenko to root out the defectors. The strike team attempts to exfil, but is captured by Kravchenko and Omega forces.

Amidst the operations at the Ural Mountains, both Requiem and Omega come into contact with Kazimir Zykov, a Soviet engineer who was originally sent to the Endstation bunker in 1945 to shut it down, and has been trapped inside the Dark Aether since then. Zykov, who wishes to escape the dimension, has attempted to reach out to the real world, giving both Requiem and Omega warnings of a mysterious entity commanding the undead forces from within. Meanwhile, Valentina continues to further her own agenda: to open a gateway to the Dark Aether in hopes of freeing her father, who seemingly has been communicating with her from the other side since her childhood. Omega Group eventually deduces Valentina's real identity as the daughter of Ulrich Vogel, a Nazi scientist who previously lead Projekt Endstation.

Two months after the strike team's capture, an outbreak occurs in East Berlin, where Valentina was last sighted. Having learned of her true allegiance, Kravchenko decides to deploy the Requiem strike team at the Berlin site to stop her, while overseeing their mission. Upon arriving in Berlin, Kravchenko and the strike team learn that Valentina has been mutated with Dark Aether energy by the Forsaken, the entity mentioned by Zykov, who was also masquerading as Vogel to trick Valentina into doing his bidding. The strike team reaches an abandoned CIA safehouse and reactivates Klaus, a combat robot customized with an artificial intelligence module created by the Director of Requiem. With Omega Group's instructions, the team constructs a miniature Aetherium warhead using components left onsite by the CIA. Valentina attempts to stop them, but is ultimately defeated, and her energy is used to refine the Aetherium for the warhead. As the Forsaken taunts Requiem of his imminent arrival, Klaus carries the warhead through the portal to complete the mission. Kravchenko attempts to betray the strike team at the last minute, but Maxis, using her Dark Aether power, manages to open a portal, allowing the team to return home safely. Meanwhile, the Director monitors Maxis, and sends a group memo to an unknown recipient, noting her growing power as a concern toward Project Janus.

As Operation Threshold expands into the North Atlantic Sea and Algeria, the Director continues to pressure Maxis in isolation, coercing her into using her powers. Meanwhile, Omega Group authorizes a new operation to free Zykov from the Dark Aether, intending to use this opportunity to take down the Forsaken with their own warheads. Requiem, after receiving intel on Omega's new operation from Ravenov, also intends to free Zykov by their own means. On June 4, 1985, the Requiem strike team is deployed to an Omega test site in Ukraine, where Kravchenko and Peck are conducting the final steps to open a Dark Aether gateway. They succeed in freeing Zykov, only to learn that he was the Forsaken all along. As Kravchenko and Peck attempt to escape the facility, Maxis and the strike team make their final stand against the Forsaken. Eventually, Maxis sacrifices herself by plunging into a Dark Aether portal, weakening the Forsaken enough for him to be captured by Omega's containment chamber. With the Forsaken defeated, all global outbreak zones are collapsed, and the undead threat is contained. The Director - revealed to be Edward "Eddie" Richtofen - orders Requiem to be shut down, and its department leads apprehended alongside the strike team, while the Forsaken's chamber is delivered to an unknown location. Five years later, Peck travels to Japan and charters a boat to the middle of the Pacific Ocean, claiming that he is looking for "some old friends".