Metal Gear Solid 4 is set in 2014, nine years after the plot of Metal Gear Solid and five years after Metal Gear Solid 2: Sons of Liberty. The world economy relies on continuous war, fought by PMCs, which outnumber government military forces. PMC soldiers are outfitted with nanomachines that enhance their abilities on the battlefield. The control network created through these nanomachines is called Sons of the Patriots (SOP), and Liquid Ocelot is preparing to hijack the system. 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 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.
Act 1 – Liquid Sun
Seeking information on Liquid’s whereabouts, Snake (with remote support from Otacon and Sunny) infiltrates the area where Liquid’s army is camped and is told to rendezvous with a group of U.S. Army informants posted nearby. On his way to the meeting, he encounters Drebin 893, a black market arms dealer who injects Snake with nanomachines that enable him to use the latest generation of weaponry. At the rendezvous point, Snake encounters the Rat Patrol 01 unit, led by his old comrade Meryl Silverburgh. They exchange intelligence and prepare to move on to Liquid’s camp, but are suddenly ambushed by Liquid’s personal troops, the FROGs. Snake continues on alone to the camp, and on the way witnesses four cyborgs wreaking havoc on a group of armed militia men. Liquid unleashes a signal that incapacitates Snake, the Rat Patrol, and all other soldiers in the area equipped with nanomachines. As he collapses, Snake catches a glimpse of Dr. Naomi Hunter, who had injected him with the virus FOXDIE in Metal Gear Solid before fleeing Shadow Moses with Liquid. The only person unaffected by the nanomachine destabilizer is Rat Patrolman Johnny Sasaki, who helps Snake up and transports him to safety.
Act 2 – Solid Sun
Via an encoded message, Naomi explains she is being forced to do research for Liquid in South America and asks for Snake’s help. Snake enters the South American locale, and witnesses one of the cyborgs and Vamp turning the local rebels against him. He yet again meets Drebin, who reveals the true identity of the cyborgs: the Beauty and the Beast Corps, four female soldiers suffering from Post traumatic stress disorder with orders to kill Snake. He also explains that SOP is currently controlled by the Patriots, a network of AI cores.
Snake reaches Naomi who explains that Liquid plans to use Big Boss’ biometric data to access the Patriot’s core AI and take control of SOP. Her tests indicate Snake’s rapid aging is genetic, and that the FOXDIE virus will cost him his life within six months. Before that, however, Snake will start spreading a deadly mutated version of FOXDIE, effectively becoming a biological weapon. Naomi is kidnapped by FROGs, leaving Snake to battle Laughing Octopus. Snake later tracks Naomi down and they make their escape with the help of Drebin. When they end up surrounded by Gekko. Raiden, now a cyborg himself, appears to assist them with his sword skills and, at great bodily harm, stalls Vamp, his nemesis from MGS2, ensuring their escape.
Safely aboard the Nomad, the team decides to get medical treatment for Raiden in Eastern Europe.
Act 3 – Third Sun
Naomi builds a friendship with Sunny and shares intimate moments with Otacon. She explains that an Eastern European resistance group possess the remains of Big Boss. Snake trails a resistance member to their leader, Big Mama, who is revealed to be EVA, surrogate mother to Snake, and his nemesis Liquid Snake, through the Les Enfants Terribles project. True to Big Mama’s prediction, the Raven Sword PMC attacks the vehicles transporting Big Boss’ remains. Snake and Big Mama’s motorcycle escort ends in a crash, forcing Snake to battle Raging Raven, a bird-like cyborg that fires guns and missiles. He subsequently helps Big Mama escape to the riverside, where Big Boss’s remains were really kept, and is confronted by Liquid. Unfazed by the military forces ordering him to surrender, Liquid destabilizes the SOP system once again, and easily claims victory in the ensuing firefight. He throws Big Boss’s body to the flames, where Big Mama follows to save it. Snake’s fruitless attempts to save Big Mama leave him with a burn scar. Liquid escapes with Naomi, but the Mk. II makes it onto their gunboat.
Act 4 – Twin Suns
Before it’s destroyed, Mk. II sends a transmission revealing Liquid’s plan. He intends to destroy the Patriots’ core AI with a nuclear strike using Metal Gear REX’s rail gun, then substitute it with his own core, and gain control. To this end, he needs a non ID-tagged warhead from the cache left in the Shadow Moses facility.
Snake returns to Shadow Moses Island (the setting of the original Metal Gear Solid), makes his way through the complex and defeats Crying Wolf and her FROGs outfit in the same field that he defeated Sniper Wolf in MGS. When he reaches REX’s hangar, he finds the rail gun has been removed and Vamp waiting for him, with Naomi at his side. Snake fights Vamp one on one, and then suppresses Vamp’s nanomachines and holds off suicide Gekko while Raiden fights and kills Vamp. Naomi, revealing she’s riddled with cancer and tormented by her mistakes, disables the nanomachines that kept her alive. Snake and Raiden use REX to head out of the collapsing hangar, but Raiden ends up pinned under its rubble. Snake, now operating his previous nemesis, 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, stalls him. Eventually, cannon fire from the USS Missouri (BB-63) forces Outer Haven to retreat.
Act 5 – Old Sun
Aboard the Missouri, Mei Ling, now a U.S. Navy Captain, orders the battleship to intercept Outer Haven. While en route to the intercept point, she explains that Liquid’s AI core is already stowed within the SOP system and must be kept on in order to remain undetected by the SOP AIs. To launch the nuke, Outer Haven will need to surface and open up its armored shell, which will create an opportunity to board the submersible and sabotage the AI core. Snake, Meryl and Johnny agree to catapult onto it and avert Liquid’s plans by implanting a virus in Liquid’s AI core. The catapult landing leaves Snake alone, and he sneaks into the control room, where he confronts and defeats Screaming Mantis, who had Meryl under her control using puppet strings. FROGs storm in, and Meryl decides to hold them back while Snake proceeds. Johnny arrives to assist Meryl, and confides he isn’t influenced by SOP due to him lacking nanomachines. Meryl and Johnny’s romance heats up in sync with the battle, culminating in the two exchanging marriage proposals. On his way to the core, Snake is aided by Raiden. The last part of the way, filled with lethal microwave emitters, Snake traverses on his own, getting weaker as he moves along. Half dead, he finally arrives at the core, where the Mk. III uploads the virus. Programmed by Naomi and Sunny, FOXALIVE destroys all the AI cores, disables the SOP system and brings the war economy to a grinding halt. It effectively counteracts the Patriots’ upcoming civilian control scheme while preserving the energy and resource networks essential to modern society.
Snake, having passed out in the core, awakes atop Outer Haven’s sail where Liquid Ocelot asserts he is ready to gain control. From there, Snake and Liquid have their final showdown, a hand-to-hand combat, from which Snake emerges triumphant.
Epilogue – Naked Sin
Meryl and Johnny’s wedding is underway, after Meryl accepts Roy Campbell as her father, forgiving him for their past. The wedding ceremony concludes with a kiss and the celebration begins. Drebin reveals that he was once a child soldier. Drebin and Rat Patrol were both pawns in the Patriots’ schemes, but are now free. Raiden, hospitalized after restorative surgery, receives a visit from Rose, who introduces him to their son. She reveals that her miscarriage and marriage to Roy Campbell were only a smokescreen to protect them from the Patriots. The three embrace as a family, with Raiden stating that he’s ‘done running’. Snake stands before the grave of Big Boss, ready to take his own life to avert becoming a biological weapon. Snake sticks his pistol in his mouth and the camera turns away. A gunshot is then heard followed by bits falling in the dirt.
Debriefing – Naked Sun
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, Para-Medic, 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. He also explains that Ocelot purposefully used nanomachines and hypnotherapy to implant the persona of Liquid Snake as his own. Over the years, Zero let the newly established AI network assume more and more control, eventually leading to dependence on the war economy, a vision far from The Boss’ original will. Big Boss puts an end to the last remnant of this false vision by shutting down Zero’s life support unit thus killing Zero.
Big Boss informs Snake that the nanomachines Drebin 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 before his own death. Big Boss succumbs to FOXDIE, but not before he makes amends with Snake.
When all is settled, Snake decides to live out his life peacefully, in the company of Otacon and Sunny, and vows to see this new age off.