- Set in 2025, new unmanned machines have been taken over by Nicaraguan terrorist, Raul Menendez, forcing the U.S.A. to take action.
- Taken place ten years after the first black ops, Alex mason, Sgt.Frank Woods and Jason Hudson are back in the biggest call of duty event. Later on the creators take you to 2025 where the military technology is being hacked by a notorious villain, Raul Menendez. its up to David mason and Harper to stop Menendez before he takes over the entire world—Anonymous
- Set in 2025, US Navy Seal Commander David 'Section' Mason, the son of former CIA Operative Alex Mason, fights to take out Raul Menendez , a Nicaraguan narco-terrorist and his organization, Cordis Die, after Menendez manages to gain control of the entire Unmanned US Drone Fleet in order to launch attacks on cities across the world. Meanwhile, Sergeant Frank Woods, now retired, recalls his experiences in the 1980s with Alex Mason on why Menendez became a terrorist.
- The story is told through connecting events in the 1980's and the 2020's.
In 1986 Alex Mason is living in Alaska with his son David, they have a rocky relationship which is tensed when CIA operative Jason Hudson calls Alex back into action to find Sergeant Frank Woods, he disappeared with American soldiers in Angola investigating an arms smuggling ring. Mason and Hudson aid UNITA and Jonas Savimbi in their fight against the MPLA in exchange for Woods location, he's being held aboard a barge in the Cubango river which belongs to a Nicaraguan arms dealer. Hudson and Mason take the barge and find Woods in a container with the rotting corpses of his compatriots.
A Hind gunship attacks the barge which Mason shoots down and the barge hits dry land, the three operatives move further inland to a radio tower which is under occupation of Cuban troops. Mason infiltrates the tower to call for help and encounters the Nicaraguan, Raul Menendez giving orders to Lev Kravchenko in Afghanistan. Mason orders Menendez to change frequencies but Menendez merely smashes the radio and challenges Mason, Cuban troops walk in and Mason takes Menendez hostage, the latter pulls the pin on a hand grenade, Menendez and Mason struggle and Mason shoots Menendez in his right eye. Mason, Hudson and Woods retreat back to the river when Savimbi arrives in a Hind to rescue them.
Mason and Woods are deployed in Afghanistan to aid the Mujahedeen against the Soviet occupation, Jason Hudson and a Chinese operative, Tian Zhao, are there also. A Soviet attack on an Afghan camp is repelled, Lev Kravchenko shows up in a heavy tank that Mason destroys, the return of Kravchenko causes the numbers to appear in Mason's head again and Viktor Reznov's voice demanding Kravchenko be killed. Kravchenko is taken for questioning, throughout Mason keeps hearing the numbers and has to fight the urge to shoot Kravchenko, should the player resist, Kravchenko will divulge enough information on Menendez' dealings and that he has spies everywhere, including the CIA. Woods shoots him only for the Mujahedeen to turn on them, Menendez having told them that America will betray them eventually and the three Americans and the Chinese are left to die in the desert until a rescue arrives.
Later the U.S. becomes friendly with Panamanian leader Manuel Noriega, a raid is conducted on the Menendez estate in Nicaragua, where Raul is caring for his sister, Josefina, whom had been disfigured in a fire in their youth. The Panamanian troops take Raul prisoner only for Noriega to release him as a future favor, Raul beats up Noriega and runs back to his home which is now on fire, fighting through the Panamanian's in a bloodthirsty rage. At the same time, the American operatives, Mason, Woods and Hudson are headed for the estate for Menendez capture, Woods is more intent on killing him. In Angola Menendez had Woods men tortured in front of him for whatever the information the CIA had on him, Woods refused and was left to rot in the container with the bodies of his men. At the estate, Raul rushes to save his sister from the fire and gets in a struggle with Hudson, Woods throws a grenade in a fit of anger which bounces off a wall into Josefina's room. The blast destroys most of the building, Josefina is dead and Raul is believed dead when carried off in a body bag.
The U.S. military invades Panama in 1989 to capture Noriega and blemish his reputation with contraband, Mason and Woods head in with the Navy Seals, Hudson is supposedly handling their mission yet his communications are erratic. Woods and Mason apprehend Noriega but Hudson changes their objective, they are to bring him to a military checkpoint for an exchange. Woods and Noriega head to a rooftop so Woods can oversee the prisoner swap through a sniper rifle, the prisoner's face is hidden under a sack and is allegedly Raul Menendez, Hudson orders Woods to shoot him in the head, or Woods can target any other part of the body. Once the shot is taken Woods heads to the body to find it's Mason, having been tricked Woods aims his gun at Noriega only for the still living Menendez to shoot Woods in both knees crippling him.
Woods is knocked unconscious and taken to a room, Menendez had kidnapped Mason's son David and coerced Hudson into manipulating his teammates, then Menendez murders Hudson leaving Woods and David with Alex's motionless body. Woods took David in after that.
In 2014 a populist movement known as Cordis Die forms under the guise of liberators of the impoverished under the guise of an anonymous and charismatic leader, Odysseus, a handle for Raul Menendez. In 2025 the United States and China are locked in a Second Cold War, David Mason is a Lieutenant Commander in SEAL Team Six under the code name "Section" and Cordis Die are now two billion strong.
Section is in Myanmar with JSOC colleagues Master Chief Petty Officer Mike Harper, Chief Petty Officer Javier Salazar and Petty Officer 1st Class Crosby. Their mission is to infiltrate an ancient temple now under PMC occupation for information on something called "Celerium." An underground lab is discovered beneath the temple, JSOC fight through the enemy and discover an employee of the TACITUS corporation, Erik Breighner in hiding, he was working on something call a Celerium chip which he gives to Section, Celerium is rare earth element, one of many, the main fuel source of the entire planet and China is the largest holder. Menendez intends to use the chip as a tool for global cyber attack, Breighner heard references to "Karma" but knows no more than that and is shot dead from a stray bullet. JSOC fights out of the lab and back to the surface where the Seals have arrived with superior officer, Admiral Thomas Briggs.
A U.S. drone is shot down in Pakistan, Cordis Die allied ISI are attempting to reverse engineer it. JSOC travels to Lahore during a flood where Menendez is meeting ISI and his second-in-command DeFalco. Section and Harper record the conversations, Menendez is aware their presence even having arranged it, the ISI are alerted and JSOC flee the scene in four-wheelers to extraction encountering Tian Zhao, now a General and leader of the Strategic Defense Coalition, a military alliance made of Asian nations. Zhao is there for Menendez, he backs out calmly once hearing of JSOC's mission.
Outside of the story, the player can partake in Strike Force missions, the Strategic Defense Coalition is expanding under Zhao's command against the wishes of Chinese government. Many countries are at risk of SDC takeovers, four major powers could be invaded and swayed to join SDC, Iran, India, Afghanistan and Russia. Should the player partake in these missions, the SDC will be repelled, the four nations and SDC will side with JSOC.
JSOC are analyzing the recordings and spot Menendez slip something to DeFalco, a card bearing the symbol of Colossus, a wealthy resort in the Cayman Islands. Section, Harper and Salazar infiltrate under the guise of union workers thanks to CIA operative Farid, Harper goes alone and accidentally bumps into an American woman, Section and Salazar break into the server room which is under PMC guard and search the servers for "Karma." The cameras find the Chinese character for karma as a tattoo on a woman's neck, the same American woman that Harper bumped into. Karma is the handle of Chloe Lynch, a hacker and former employee of arms manufacturer Tacitus.
Harper and Section track her to a disco, DeFalco arrives with mercenaries and starts taking hostages, threatening them until Lynch gives herself up, she does and the mercenaries open fire. JSOC pursue DeFalco through Colossus amidst phone triggered bombs which Farid is attempting to jam, if the player is fast enough, Section will catch up with DeFalco and eliminate him and JSOC will leave with Lynch, if not, DeFalco will leave with Lynch and another Strike Force mission will become available in which Lynch must be rescued.
Farid is a mole within Cordis Die, alongside Menendez in Yemen. Menendez is about to deliver a speech to his troops when JSOC arrives with Yemeni military, Menendez instructs Farid to go to a citadel and await further orders. Once there Menendez shoots down a V-TOL with Harper on board, Cordis Die drags him out and Farid is made to test his loyalty by shooting Harper which Harper will goad him to.
Farid can try to shoot Menendez only to be killed himself, or shoot Harper, both occur just as Section arrives with Salazar, fighting through Cordis Die and arresting Menendez. He is taken to the aircraft carrier the USS Barack Obama, Briggs will be talking with Defense Secretary David Petraus, depending on player choices in the Strike Force missions the U.S. will either be on better terms with China or at DefCon 3. Menendez is taken for interrogation but will speak only to Section, their discussion is cut short when Cordis Die launches an attack on the Obama and the fleet, Menendez somehow escapes his handcuffs and takes Salazar hostage, coercing Section into lowering his weapon, Menendez knocks him out and flees.
Section and Salazar hurry to find Briggs, fighting through the invading force, they separate, Salazar heads to the server room where Briggs is trying to reboot the automated defenses, Section finds the surveillance room giving a view into the server room where Briggs is about to reboot. Menendez is outside with a follower (or DeFalco if alive), he takes Briggs hostage and holds up everyone in the server room which include Salazar, Lynch (if resscued) and Farid (if alive.)
Salazar shoots two sailors and possibly Lynch if Farid is unavailable, he will sacrifice himself to save her and or kill Falco. Menendez can either kill or injure Briggs then upload a virus to the U.S satellite network giving control over their drone fleet. Mason has witnessed Salazar's treachery, the sailors help him break into the server room, Lynch can attempt to fix the virus and Briggs can offer advice to Mason (if both are alive.) Menendez escapes in a stolen jet, Salazar willingly surrenders himself to the Navy, if Harper is alive he'll kill Salazar. Mason commanders a jet to fly to the American president. If the Strike Force missions were completed the Chinese Air Force will appear to repel the attacking drones and if Briggs was spared, the ship's defenses are reactivated, saving the carrier. If one or neither happened the carrier will be sunk killing all hands.
In Los Angeles President Marion Bosworth is conversing with Chinese Premier Chen from her limousine, if the Americans and Chinese have reconciled, Bosworth promises to aid China against Menendez, if acrimonious, Chen will disbelieve that the hostile American drones have been hacked. Mason (and possibly Harper) and the Secret Service are escorting President Bosworth to a bunker, their convoy is attacked by the hacked drones, Mason protects Bosworth from drone and Cordis Die attacks eventually getting her to safety.
Menendez has been tracked to a facility in Artibonite, Haiti. Mason is leading a combined military assault on the facility (with possible help from the Chinese.) The forces seize a control room where a live broadcast from Menendez begins, he destroys all the drones removing the U.S. drone superiority and urges his followers to rise. The self-destruct is activated, Menendez has stolen a JSOC uniform to sneak past military checkpoints, Mason intercepts and holds a gun to his head, the player can either shoot or arrest him.
Depending the numerous player choices in the game the endings are varied.
If Lynch is alive she able to crack the Celerium worm undoing Menendez cyber attack for which she'll be honored and appearing as a guest on Jimmy Kimmel Live. If dead the worm will remain undecrypted. If Menendez is alive and the worm was cracked, Lynch will mock him on T.V. for which Menendez will throw a tantrum. If the worm is still active, the cyber attack will commence, all power across the world will be disrupted, Menendez will escape his cell, find and kill Woods, then visit Sofia's grave and immolate himself.
If Menendez was killed, he'll be martyred and Cordis Die will revolt globally.
If Alex Mason is dead, David "Section" attends his grave with Woods and declare his retirement. If Alex is alive, he'll reappear before an unbelieving Woods, David arrives to see his father who compliments him on his career.
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