Five years have passed since the events of the first game. Despite the SAS and USMC’s best efforts and the death of Imran Zakhaev, the Ultranationalists won the Russian Civil War and assumed power of the country, with a statue of Zakhaev erected in Moscow's Red Square declaring him the "Hero of the New Russia", making him a martyr. But contrary to the US and UK’s fears, the Ultranationalists do not immediately attack either country and instead try to look for peaceful ways to rebuild their trust.
In Afghanistan, Sergeant Foley leads a training session with the Afghan National Army while Private First-Class Joseph Allen runs a session in the Pit under the watchful eye of General Shepherd. After the US Army Rangers rescue a unit from the OpFor in The Red Zone, Shepherd recruits Allen to join an elite task force called Task Force 141. The Task Force is comprised of elite soldiers from different countries who partake in special assignments. Two operatives, John “Soap” MacTavish (who was promoted to Captain after the events of the first game) and Sergeant Gary “Roach” Sanderson, infiltrate a Russian base in the Kazakhstan Tian Shan Mountains to recover an ACS module from a downed satellite, successfully doing so despite being compromised by Spetsnaz.
Shepherd gives Allen an undercover assignment to investigate the Russian Terrorist Vladimir Makarov, a former Ultranationalist removed from power after the current leader thought his ideals went against their peaceful ones. Furious to be betrayed by the party he stood for, Makarov swore to make Russia and the Western countries pay. Makarov leads his terrorist cell in a massacre at the Zakhaev International Airport, killing hundreds of innocents and security personnel who tried to stop them. As they escape from the airport, Makarov shoots Allen at point-blank range and leaves the latter for dead as he figured out Allen was a mole. Allen’s body is found by personnel, and his presence causes outrage from Russia.
Because Task Force 141 knows the truth about the massacre, they go to Rio de Janeiro, Brazil, to locate the arms dealer who supplied Makarov with the weapons: Alejandro Rojas. Soap, Roach, and fellow Task Force member Simon “Ghost” Riley, search for Rojas in the Favela, managing to apprehend him and interrogate him for information. The only thing they get out of Rojas is that there is someone who hates Makarov more than Shepherd and is currently imprisoned in the Gulag. Soap’s team manages to escape the Rojas’ Militia forces thanks to Nikolai providing extraction.
Meanwhile, the Russians invade the US in response to the massacre, attacking multiple States and cities as revenge. Foley’s team, which includes Corporal Dunn and Private Ramirez, return from Afghanistan to protect their country, fighting through the streets of Virginia to stop the Russian invasion. Eventually, General Shepherd takes command of the US Army Rangers and dispatches Foley’s team to recover an HVI with intel that could help them. However, Foley’s team discovers the HVI dead, with the body of one of Makarov’s men next to him.
With the intel from Rojas, Task Force 141 heads to the Gulag in Russia to rescue Prisoner 627. With the help of a team of Navy SEALS, Soap and his squad clear an oil rig to enter the Gulag and search for the prisoner. They searched high and low for Prisoner 627, and eventually, they found him: Captain John Price. Having been imprisoned in the Gulag after the failure of a previous mission, Price reunites with Soap and the others before they escape the collapsing Gulag.
With Price back on Task Force 141, he leads a mission to help the American Soldiers with the Russian Invasion despite Shepherd’s insistence that they go after Makarov. Price takes Roach and Ghost to secure a submarine near Petropavlovsk, Russia, and they manage to make it to the naval base where the vehicle is. However, to the shock and horror of Ghost, Price uses the commandeered submarine to fire an SLBM into the sky to who knows where.
Back in America, Foley’s team has moved to Washington D.C. to drive out the Russian forces, but it is not going well, as the city is being overrun, civilian evac transports are being decimated by the Revenge-driven Russian troops, and D.C. is on the verge of collapse as U.S. forces are being forced to pull out as their positions are overrun. Despite their best efforts, the team is overwhelmed by Russian troopers and are nearly killed if not for Price’s plan. It turns out that Price launched the SLBM to the International Space Station, destroying it and causing an EMP across the East Coast of America. The EMP disables all the electronics in the area, including in Washington, but it was thanks to Price that it saved the U.S. forces defending D.C. from being wiped out, as with all means of air support and armor destroyed or disabled by the EMP, the Russians have lost the initiative as fresh support is miles away. Despite having no tech, Foley leads the US Army Rangers in retaking the White House and driving the Russians out of Washington D.C.
Due to Makarov being a high-value target, Shepherd receives a blank check from the Pentagon to use any resource they have to take the former out. Task Force 141 splits up to two different locations Makarov could be hiding at: Price and Soap’s group going to the boneyard in Afghanistan, while Roach and Ghost’s group going to the Caucasus Mountains. Roach and Ghost’s group reach the safehouse but find nobody there. Fortunately, they download Makarov’s intel through a DSM and make it to the extraction point as Makarov’s men chase after them. But when Roach and Ghost make it, Shepherd suddenly shoots Roach and Ghost before having his Shadow Company burn their bodies. Roach’s last moment is hearing Price futilely warning them about Shepherd’s betrayal as he and Soap are compromised as well.
Under fire from both Makarov’s men and Shepherd’s Shadow Company, Soap and Price fight through the boneyard and meet Nikolai for extraction. On the way there, Price contacts Makarov and asks the latter to track Shepherd for them, as the General will kill both in a matter of time. Makarov relents and gives Price and Soap Shepherd’s location: Site Hotel Bravo. With this information, Price and Soap engage in a one-way mission to kill Shepherd as payback for backstabbing them and being responsible for the death of their allies.
Price and Soap sneak into Site Hotel Bravo, killing off Shepherd’s Shadow Company along the way, before chasing after the General in a Zodiac. The two stop Shepherd from escaping in a Pave Low, but they fall down a waterfall and are separated. Once Soap regains conscience, he hunts for Shepherd and tries to stab him, only for the General to knock him off his feet and stab him in the chest. As Shepherd prepares to kill Soap, he reveals he did all of this, betraying Task Force 141 and using Allen as a pawn to get the Russians to invade the US, to reignite the American army as the toughest Global power after losing 30,000 soldiers in the nuclear explosion five years ago. Price arrives and attacks Shepherd, leading to a fistfight between the two. Soap uses this opportunity to pull the knife out of his chest and flings it at Shepherd’s head, killing the treacherous General. Afterwards, Nikolai arrives and gets Price and Soap out of the area and give the latter proper medical treatment.
