We finish now this story with the last game of the saga : MGS 4.

The story takes place in 2014, five years after the incident in Manhattan (MGS 2), in a world where military interventions in foreign countries are restricted, causing the emergence of private military companies (PMCs). The war and its economy are controlled by the Sons Of the Patriots (SOP) system, an AI that governs every soldier and weapon through nanotechnology. At the head of the five largest PMCs, Liquid Ocelot (Liquid Snake has totally taken control of Revolver Ocelot) plans to hijack the system in order to raise an insurrection against the Patriots and pursue Big Boss’ idealistic intentions.

Snake, meanwhile, is experiencing accelerated aging due to his status as a clone, and has less than a year to live. When his former commanding officer Roy Campbell (from MGS 1) approaches him with one last mission : to terminate Liquid, Snake accepts and is dropped into the Middle Eastern war zone where Liquid is believed to be hiding.

The hero is going to the Advent Palace where he will meet the U.S. Marines’ informants : The Rat Patrol Team 01. The team is led by Meryl Silverburgh, old friend of Snake and Colonel Roy Campbell’s niece. Then Snake succeeds in locating Liquid in a camp. But when he’s preparing to eliminate him, a strange uneasiness seizes him and all the soldiers on the spot, causing them to collapse in grief and remorse or fight between themselves… Liquid has made a first attempt to hack the SOP system. Snake receives a serum from Naomi Hunter (she had injected him the FoxDie virus just before MGS 1, believing he had killed her brother), then he’s discharged by the Rat Patrol Team.

Then Otacon discovers a video message sent by Naomi Hunter. We see her held hostage in South America. Snake infiltrates the area and learns that the Patriots have now formed a network of five AIs : GW (supposedly destroyed in 2009), TJ, TR and AL, which operate under the supervision of the Central AI JD (all names are the initials of U.S. Presidents). Snake finds Naomi, who tells him that eventually, the FoxDie virus won’t threaten only those for which it was intended, but any person, transforming Snake into a “mass destruction walking weapon”. A little while later, Snake meets Laughting Octopus, a member of the Beauty and the Beast (B&B) group, which works for Ocelot. After killing her, he and Naomi find themselves surrounded by PMC soldiers, Gekkos (robots that look like small Metal Gear) and … Vamp! Indeed, Vamp is immortal thanks to his nanomachines, and wasn’t killed by the headshot he received from Raiden fives years ago! Fortunately, Raiden intervenes and allows Snake and Naomi to escape. The fight between Raiden (now a cyborg ninja) and Vamp doesn’t give a winner. Vamp injured, falls asleep, while Raiden seriously injured, is evacuated by Snake.

Next Naomi reveals that Big Boss is clinically alive, at least its cells, and his brain is blocked by nanomachines. Her body is held by a rebel group called Lost Paradise, located in Eastern Europe. Their leader, Big Mama, is in fact Eva (from MGS 3), surrogate mother of Solid Snake, Liquid Snake and Solidus Snake. She also reveals the origins of the Patriots, founded by Major Zero (Big Boss’ commander in MGS 3) forty years earlier. Then Snake confronts and kills Raving Raven, another member of the B&B unit. Afterwards they go on a boat where Big Boss’ body is located. However, the boat is destroyed by Liquid Ocelot, who breaks down all U.S. military’s weapons in controlling the SOP system. He throws Big Boss’ body in the fire, and Eva, in an attempt to save him, is badly burnt. She dies in Snake’s arms shortly after.

Liquid Ocelot intends to destroy JD, the Patriots’ core AI, with a nuclear strike, then substitute it with his own core, and gain control. To this end, he needs the only remaining non ID-tagged warhead, the Metal Gear REX’s railgun, in the Shadow Moses facility. So Snake returns to Shadow Moses, to prevent Liquid from stealing the REX, where they faced off nine years earlier. He meets Crying Wolf, third member of the B&B unit, and defeats her in the same place he had killed Sniper Wolf in MGS 1. When he reaches REX’s hangar, Vamp is waiting for him. He fights Vamp one on one, and then suppresses Vamp’s nanomachines, which made him immortal. Thanks to this, Raiden fights Vamp again, and kills him, once and for all! Naomi, revealing she’s riddled with cancer and tormented by her mistakes, disables the nanomachines that kept her alive. Then Snake, operating REX, is left to duel with Metal Gear RAY, piloted by Liquid. After both Metal Gears are destroyed, Liquid reveals Outer Haven, a submersible warship ready to fulfill his launch plan. Liquid uses this weapon as a ram to kill Snake, but Raiden, who cut off his arm to free himself, saves him.

Snake then penetrates the warship to enter the server room containing the GW system and to introduce a computer virus designed by Naomi and Sunny (Olga Gurlukovich’s daughter) to stop the nuclear strike on JD. On the way, Snake crosses paths with Screaming Mantis, last member of the B&B unit, and after killing her, manages to insert the virus, which destroys not only GW but also all the Patriots AI components, disabling all the defense systems of Liquid’s troops. Then Liquid Ocelot finds Snake on Outer Heaven’s roof, and he reveals to him his true intentions. All that Snake has successfully succeded in doing was prepared and supervised by Liquid. The Patriots had planned that Snake would kill Liquid, giving them total control of the SOP system, but they didn’t expect Snake to destroy the system. He pretended to be possessed by Liquid so that the Patriots would not suspect him, leaving Snake to inject the virus. Following this revelation, they engage in an epic battle, which Solid Snake wins.

His mission over, Snake meditates on The Boss and Big Boss’ graves and then prepares to kill himself to stop the FoxDie mutation. This suicide is, in his own words, his « last mission ».  Yet Snake does not end his life.Big Boss, very much alive, appears and explains that the body burned in Eastern Europe was actually that of Solidus Snake and reveals that the Patriots were originally an interpretation of The Boss’ will, founded by Major Zero, Eva, Ocelot, Sigint (who helped Big Boss in MGS 3), Para-Medic (who gave medical instructions to Big Boss during the Snake Eater operation), and Big Boss himself. With increasing power, two rival factions arose within the Patriots’ ranks, Zero’s who stood for complete control, and Big Boss’, who dreamed of a soldier’s world. Eva and Ocelot joined Big Boss in his cause.

Big Boss informs Snake that the nanomachines, that were injected into him included a new strain of FoxDie, programmed by the Patriot AIs to kill the rival Patriot faction and eradicate the old versions of FoxDie. Thus, Snake has no risk of becoming a biological weapon, at least not before his own death. Big Boss succumbs to FoxDie, but not before he makes amends with Snake.