Metal Gear Solid 3: Snake Eater
"Virtuous Mission"

Metal Gear Solid 3 is set during the Cold War in 1964, where Naked Snake is sent to the jungles of the Soviet Union. Aided over radio by Major Zero, Para-Medic, and his former mentor The Boss, his mission is to rescue a defecting Soviet scientist named Sokolov who is secretly developing an advanced nuclear-equipped tank called the "Shagohod." The mission goes smoothly until The Boss defects and provides her new benefactor Colonel Volgin with two Davy Crockett miniature nuclear shells. Sokolov is captured by the Cobra Unit and Snake is heavily injured in combat by The Boss, allowing Volgin and his cohorts to escape with Sokolov. Volgin detonates one of the nuclear shells to cover up its theft, which is subsequently blamed on The Boss.

"Operation Snake Eater"

Having detected the US aircraft which deployed Snake flying over Soviet soil, the Soviet Union declares the United States responsible for the atomic attack, tipping both nations to the edge of a nuclear war. In a secret conference between US President Lyndon Johnson and Soviet Premier Nikita Khrushchev, a deal is hatched to prove the US's innocence and restore peace. The United States agree to stop Volgin's renegade faction, destroy the stolen Shagohod and eliminate the American defector, The Boss.

A week after being rescued from the region, Snake is redeployed into the Soviet jungle as part of Operation Snake Eater, to fulfill the United States' promises. During the mission, he gains the assistance of another American defector, ex-NSA agent EVA, who defected a few years earlier. After numerous encounters with the elite Ocelot Unit (led by a young Ocelot), and defeating nearly every member of the Cobra Unit, Snake succeeds in locating Sokolov and the stolen Shagohod, only to be captured in Volgin's military fortress, Groznyj Grad. After witnessing the apparent death of Sokolov, Snake is tortured and has his eye injured when Ocelot shoots to kill EVA; Snake ultimately escapes.

When he returns to the facility to destroy the Shagohod, Snake learns of The Philosophers. Made up of the most powerful men in the United States, Soviet Union, and China, they are an Illuminati-like organization who control the world behind the scenes. However, after the end of World War II, they began to fight amongst themselves, and the organization broke down. The Philosopher's Legacy, a fund the organization had jointly amassed to finance their wars ($100 billion, about $1 trillion today when adjusted for inflation) was divided up and hidden in banks all over the world. Volgin had illegally inherited this money, and Snake learns that the US is attempting to retrieve it.

Snake continues his mission, destroying the facility and the Shagohod tank, while engaging Volgin, who is killed by a bolt of lightning during the battle. Snake and EVA travel to a lake, where a ground effect vehicle is hidden. Before they use it to escape the region, Snake confronts his old mentor, The Boss, whom he must kill to complete his mission. During this time a cut scene is shown stating that The Boss gave birth to a child (the father being The Sorrow) during a battle. Before this time however, during a radio call, EVA tells Snake that the reason Ocelot achieved the rank of major at such a young age was due to the fact that his parents were legendary soldiers. She also tells Snake that Ocelot's mother needed to cut Ocelot out during the birth, leaving a snake-like scar. This scar is seen on The Boss, which strongly suggests that she is Ocelot's mother. After an emotional battle, Snake overcomes his feelings and defeats her. He and EVA escape to Alaska, and spend the night together. During the night EVA disappears, and leaves behind a tape revealing herself to be a Chinese spy sent to steal the Philosophers Legacy for China. The tape continues, and EVA reveals that The Boss did not defect to the Soviet Union; rather, she was under orders to pretend to defect so she could infiltrate Volgin's ranks and find the location of the Legacy, which could be brought back to America. The final part of her mission was to sacrifice her honor and die at the hands of Snake, under the guise of a traitor, to prove the US's innocence in Volgin's nuclear attack from the beginning of the game.

Snake is awarded the title of "Big Boss" and given the Distinguished Service Cross for his efforts before an enthusiastic crowd; however Snake has become so distraught and demoralized after EVA's revelation that he leaves almost immediately after getting his medal, hardly acknowledging the President or Major Zero and the support staff. Later, he arrives at an anonymous grave, The Boss', just one of thousands located in Arlington Cemetery. Laying down The Boss' gun and a bouquet of lilies upon the nameless gravestone, he scans the endless rows before him, salutes, and sheds a single tear.

After the credits roll, Ocelot is heard talking (a telephone conversation), and reveals that the microfilm containing the information on the Philosopher's Legacy given to EVA was a fake, that Ocelot himself was ADAM, that half of the real legacy is in the hands of the US Government thanks to Snake, and that he was working for the CIA.

Metal Gear Solid: Protable Ops
Six years after the events of Metal Gear Solid 3, Naked Snake's former team, FOX Unit, has broken their allegiance with the CIA and gone rogue. Snake himself is also targeted by the FOX Unit, which sent renegade FOX Unit soldiers to attack and capture him. The game begins with Snake being tortured and interrogated by one of the members of FOX, Lieutenant Cunningham, who's trying to locate the whereabouts of the missing half of the Philosopher's Legacy, with the United States Government having already acquired the other half of the Legacy from the Soviet Union at the conclusion of Snake Eater. Snake is imprisoned in a cell next to Roy Campbell, the sole survivor of an American Green Beret team sent in to investigate the base. Snake learns through Roy that they're on the San Hieronymo Peninsula, the site of an abandoned Soviet missile silo in Colombia.

The two escape and Snake makes his way to a communications base, where he attempts to contact his old CO, Major Zero. Instead, he is greeted by his old FOX comrades Para-Medic and Sigint, who reveal that Snake and Zero are being accused of instigating the revolt and that the only way for Snake to clear their name is to find and apprehend the leader of the rebellion, Gene. To complicate matters, Gene has also convinced most of the Russian soldiers stationed on the base to join their side by simply taking over the chain of command of a former Red Army unit, that was secretly stationed inside the Colombian territory. In order to complete his mission, Snake must persuade enemy soldiers to join his ranks because of the scale of his mission.

Snake and his squad defeat the top members of the FOX unit and eventually they make their way into Gene's guesthouse. Snake learns many things on his way. Cunningham was working for the Pentagon and wanted Snake to push Gene into launching a nuke to Russia to prolong the Cold War. Gene was actually aware of this plan the whole time from information from Ocelot. Gene really wanted to launch a nuke at America to destroy the Philosophers and to make his nation of soldiers, "Army's Heaven". Snake destroys an experimental model of the ICBMG (the Metal Gear model) codenamed RAXA and eventually defeats Gene, destroying the ICBMG itself afterwards. After Gene is defeated he gives Big Boss the funds, equipment, personnel, and all other information regarding Army's Heaven, telling him that one day, he will need to use them. On his return home, Snake is awarded for his actions and establishes FOXHOUND afterwards. In the end, Ocelot kills the DCI and takes the documents containing the identities of the Philosophers to "end them". After the credits, Ocelot speaks with an unknown man on the phone. Ocelot speaks of using the Legacy to form the Patriots in place of the Philosophers. Ocelot actually wanted the trajectory data of the nuke to point to the DCI so he would bring the documents right to him. Ocelot requests Big Boss be able to 'join' them (he and the man on the phone) in their new endeavor - becoming the Patriots. This mysterious man, whose identity is hinted as the "man with the same codename as Null"[25] is revealed to be Major Zero in Metal Gear Solid 4: Guns of the Patriots.

Metal Gear
In the year 19XX (later established to be 1995 in Metal Gear Solid), 200km north of Galzburg, South Africa, lies Outer Heaven, a fortified state founded by a "legendary mercenary". Word had gotten out to the western world that deep within the Outer Heaven stronghold, a weapon of mass destruction is being constructed. The United States government orders the high-tech Special Forces unit FOXHOUND to infiltrate the fortress, assess the situation and neutralize the threat. In his mission, FOXHOUND operative Gray Fox infiltrated the Outer Heaven stronghold. Days later, contact with Gray Fox is lost and his last transmission simply reads "METAL GEAR..."

Operative Solid Snake, FOXHOUND's newest recruit, is ordered by squad leader Big Boss to rescue Gray Fox and carry out his mission, "Operation: Intrude N313". Upon insertion into Outer Heaven, Snake makes contact with local resistance members Kyle Schneider, Diane, and Jennifer. Using all of his skills and the equipment he procured on site, he manages to rescue Fox. He learns from Fox that Metal Gear is the codename of a nuclear warhead-equipped bipedal walking tank, which can engage and dominate in all forms of combat as well as launch its nuclear warheads from any location. Outer Heaven plans to use Metal Gear to impose itself as the new world superpower.

In order to destroy Metal Gear, and topple the Outer Heaven mercenaries, Snake rescues the lead engineer of Metal Gear, Dr. Drago Pettrovich Madnar, and his daughter, Ellen. Armed with information on how to destroy Metal Gear, his skill and indomitable spirit, Snake fights through the entire Outer Heaven force. He begins to notice that traps being set for him are too precise, and wonders how information on his activities is being tracked. Moreover, Schneider is ambushed by hostiles and is presumed dead after losing contact with Snake. The final hostage Snake rescues tells him that the mysterious "mercenary leader" of the entire base is none other than Snake's C.O., Big Boss, and that Outer Heaven is under his command.
Big Boss reveals himself to Solid Snake in the game's final battle.

Upon breaching the core of the base, Snake is able to neutralize Metal Gear before it reaches completion. As he makes his way out of the compound's basement, he is confronted by Big Boss himself; the corrupt leader had been using his connections within the U.S. government to steal military intelligence, establish his own mercenary force, and fund his activities. It was his aim to have Outer Heaven become the world's most powerful nation, able to bring even the western nations to their knees. He had the rookie Snake sent in, hoping to have him captured and feed the U.S. government misinformation, but had quite obviously underestimated Snake's capabilities.

Having lost Metal Gear and much of his force, Big Boss starts the self-destruct sequence for the compound, and promises he will not die alone; Snake will join him. An underground battle ensues, and despite injury, Snake defeats Big Boss and escapes the Outer Heaven compound as it crumbles in flames behind him. After the ending credits, a message from Big Boss is displayed saying that he will meet Solid Snake again.

Metal Gear 2: Solid Snake
By 1999, the Cold War had thawed, and nuclear disarmament by the major world powers promised a bright beginning to the 21st century. Despite this, all was not well in the world. A series of shocks to the oil market spurred the development of new high-tech energy sources, including fusion power. However, most vehicles still relied on oil for power.

Oil reserves were at a critical low, and the world community was prepared to take drastic measures, either by drilling into sand and shale for more oil, despite the difficulty -- or moving on to renewable fuels.

Such steps proved unnecessary when Czech scientist, Dr. Kio Marv, successfully bio-engineered a new species of algae, OILIX, that could produce petroleum-grade hydrocarbons with little expense and effort. Marv presented the algae to the World Energy Conference in Prague, and was on his way to a demonstration in the United States when he was kidnapped by soldiers from Zanzibar Land. NATO discovers that Zanzibar Land's leaders plan to hold the world hostage by controlling the supply of oil and nuclear brinksmanship, via a stockpile of nukes raided from nearby missile sites.

Solid Snake is brought out of retirement by FOXHOUND's new commander, Roy Campbell, and is sent to Zanzibar Land to rescue Dr. Marv.

On the course of his mission, Snake teams up with Holly White, a CIA operative posing as a journalist, and Gustava Heffner, an StB agent and Dr. Marv's bodyguard. He is also reunited with Dr. Drago Pettrovich Madnar, the Metal Gear inventor from Outer Heaven, who claims to have been once again kidnapped and forced to work on another Metal Gear project (named Metal Gear D) for Zanzibar Land, as well as oversee mass-production of smaller, non-nuclear-equipped Metal Gear units. Snake learns from Dr. Madnar that Big Boss, Snake's former FOXHOUND commander, has survived and is the man in charge in Zanzibar Land.

Upon reaching the suspension bridge leading to the Detention Camp, Gustava is killed by a missile fired by Metal Gear D and Dr. Madnar is recaptured by the enemy. The new Metal Gear's pilot is revealed to be none other than Snake's former mercenary buddy Gray Fox. Determined to finish his mission, Snake fights against Zanzibar Land's elite mercenary force and manages to reach Dr. Marv's cell. Solid Snake confronts Gray Fox in one of the game's final battles.

Snake arrives too late, unfortunately, as he finds the corpse of Dr. Marv, who was unable to survive the repeated torture. Dr. Madnar is also there and explains he was unable to save him. Just before Snake could retrieve the OILIX formula left by Dr. Marv, Holly reveals via a radio message that Dr. Madnar was not captured after all, but voluntarily resumed his work on Metal Gear and was personally overseeing its development. After the truth comes out, Dr. Madnar attacks Snake, but fails in killing him.

With the OILIX formula in Snake's hands, Snake is confronted by Gray Fox piloting Metal Gear D. After successfully destroying Metal Gear D, Snake finds himself in a minefield. The two engage in hand-to-hand combat against each other, and Snake eventually emerges as the victor.

Upon defeating Fox and retrieving the OILIX formula, Snake is met by Big Boss while trying to escape. Having lost his equipment and with no weapons at his disposal, Snake is forced to improvise using the only items he can find, a lighter and aerosol can. Fashioning a makeshift flamethrower, Snake defeats Big Boss for the second time. Snake and Holly escape together, and they deliver the OILIX formula to Campbell.

Metal Gear Solid
The game is set in 2005, where FOXHOUND and a genetically enhanced next-generation special forces unit lead an armed uprising on a remote island in Alaska's Fox Archipelago. This island, codenamed Shadow Moses, is the site of a nuclear weapons disposal facility. The forces that seized this island have acquired the nuclear-capable mecha Metal Gear REX, and are threatening the US government with a nuclear reprisal if they do not receive the remains of the "legendary mercenary" Big Boss within 24 hours.

As the game begins, Solid Snake is dispatched at the request of Colonel Roy Campbell to penetrate the terrorists' defenses and neutralize the threat. Snake is also ordered to locate hostages DARPA chief Donald Anderson, and ArmsTech president Kenneth Baker. After being found, the DARPA chief informs Snake of the new Metal Gear REX unit housed at the facility, but then suddenly dies of what appears to be a heart attack. Snake then finds the other hostage, Kenneth Baker. Revolver Ocelot challenges Snake to a gunfight, which is interrupted by a mysterious cyborg ninja who cuts off Ocelot's hand. Baker briefs Snake on the Metal Gear project and, like the DARPA chief, suddenly dies of a "heart attack".

Snake then contacts Meryl via radio, and agrees to meet her in the base's warhead disposal area on the condition that he contacts Metal Gear's designer, Hal "Otacon" Emmerich. Snake locates Otacon in his lab. The ninja reappears, and Snake realizes that it is actually his former ally Gray Fox, whom he believed killed years earlier. Otacon agrees to aid Snake remotely, using special camouflage to procure information and supplies while he remains invisible. Snake meets with Meryl and agrees for her to accompany him on his mission. Meryl gives Snake a PAL key and they head for the underground base. Part way through the base, Sniper Wolf ambushes them, wounds Meryl, and captures Snake.

While imprisoned, Liquid confirms Snake's suspicion that they are twin brothers. Snake is tortured by Ocelot and the player can choose to give in to this torture, or not. Eventually Snake is able to escape.

Snake descends into the bowels of the Shadow Moses facility. He discovers that the man that he thought was the DARPA chief was actually FOXHOUND member Decoy Octopus in disguise. Shortly after, Master Miller calls and reveals that Dr. Naomi Hunter, a support agent, has given Snake the genetically engineered virus "FoxDie" during his mission preparations, and is sending coded messages into the facility. Campbell swiftly orders her arrest. The virus, designed to kill people with particular genetic markers via cardiac arrest, was responsible for the deaths of Octopus and the ArmsTech president. Naomi contacts Snake and confesses that she joined the mission to sabotage it. But upon learning of Snake's own past, she no longer had the heart to kill him directly having reprogrammed the virus.

Infiltrating Metal Gear's hangar, Snake overhears Liquid and Ocelot preparing the launch sequence for Metal Gear REX. Thinking he is deactivating it, using the PAL key, Snake activates Metal Gear REX. Master Miller then reveals himself to be Liquid in disguise. He informs Snake that his entire mission was manipulated by the renegades to allow the launch of the nuclear weapon. Liquid explains that they are the product of the Les Enfants Terribles project, a government sponsored effort to clone Big Boss, that was conducted during the 1970s. Liquid explains that Solid received all of Big Boss' dominant alleles,while he received all the recessive alleles.

Snake destroys Metal Gear REX and defeats Liquid. He is then reunited with Meryl or Otacon, depending on the player's actions. They escape, while being chased by Liquid, in a jeep. Liquid dies from the FoxDie virus. Colonel Campbell, briefly ousted from command of the mission, calls off a nuclear airstrike intended to obliterate the evidence of the day's events and officially declares Snake killed in action to stop the US government's search for him in the future.

There are two possible endings, depending on the player's actions during the torture sequence. If the player gives in to the torture, Snake finds Meryl dead and escapes with Otacon. If the player does not give in to the torture, Meryl survives and escapes with Snake while Otacon volunteers to stay behind and sacrifice himself to help Snake and Meryl get out, not knowing that the nuclear strike intended to hit the disposal facility would never come.

After the end credits the player finds out Snake is actually genetically inferior to Liquid and has an indeterminate amount of time left before FoxDie kills him. Ocelot is revealed to be a double agent for the President of the United States, George Sears, the third Snake, Solidus. His intention was to obtain Baker's disk containing Metal Gear's specifications and deliver it to the President, and kill whoever knew of his true motives, the reason for his "accidental" killing of the DARPA chief.

Metal Gear Solid 2: Son's Of Liberty
Sons of Liberty opens on the George Washington Bridge in New York City, in 2007, two years after the Shadow Moses Island incident, the events of the original Metal Gear Solid. Solid Snake and Otacon, now members of the non-governmental organization Philanthropy, are investigating the development of a new Metal Gear consistently described as being amphibious and having been designed as a counter-Metal Gear unit which have been built since Metal Gear REX's design was leaked. Shortly after Snake's arrival on the disguised oil tanker U.S.S. Discovery, a group of Russian terrorists under the command of Russian nationalist Sergei Gurlukovich attack the ship. After sneaking up to the bridge, Snake encounters Olga, Sergei's daughter, who has refused to leave the tanker despite being pregnant.

After he successfully tranquilizes her in combat, Snake sneaks down to the hold in order to record pictures of the new Metal Gear, RAY. Matters rapidly escalate as Revolver Ocelot betrays and murders Sergei Gurlukovich. It is revealed that Ocelot has received a new arm after Metal Gear Solid, that of the late Liquid Snake, which via unknown means causes a change in Revolver Ocelot's demeanor and behavior, with Liquid somehow 'possessing' him. Under Liquid's control he sinks the tanker, and escapes with RAY before regaining command of his body.

Plant chapter

The player finds himself in control of Raiden, supposedly operating under a reformed FOXHOUND two years after the Tanker Chapter on April 29, 2009. Initially referred to as "Snake", his orders are to rescue hostages, including the US president, from the terrorist group Sons of Liberty, backed up by the rogue anti-terror training unit, Dead Cell, who are also threatening to destroy the Big Shell clean-up facility they have seized. Raiden infiltrates the Shell via sea while SEAL Team 10 enters by air. He joins forces with SEAL Lieutenant Junior Grade Iroquois Pliskin and bomb specialist Peter Stillman to disable explosives planted on the Shell by Stillman's former pupil, Fatman, now a terrorist. While Raiden successfully eliminates Fatman, Stillman is killed as a result of one of Fatman's traps.

With the assistance of a mysterious cyborg ninja calling itself Mr. X, Raiden locates the president, and discovers that the Big Shell is actually a disguise built right on top of a new Metal Gear. Known as Arsenal Gear, it houses a powerful AI supercomputer, "GW", capable of controlling information transmitted digitally. The president also claims the democratic process is a sham, and the true rulers of the United States are an organization known as the Patriots. Revolver Ocelot kills him soon after, and Raiden proceeds to his final objective: disabling Arsenal Gear and thus halting a nuclear strike. Pliskin, having revealed himself as Solid Snake, and Emma Emmerich, an Arsenal Gear engineer, assist Raiden in attempting to destroy the "GW" AI by uploading a virus. On the way to the computer room, Vamp attacks Emma. The virus is still installed, but aborts partway through; Emma dies due to a fatal knife wound from Vamp. Snake and Raiden are left with no choice but to disable Arsenal physically. As Snake's partner Otacon escapes with the surviving hostages by helicopter, Mr. X returns, revealing itself to be Olga Gurlukovich, and knocks Raiden unconscious.

Awakening naked in an Arsenal torture chamber, Raiden is probed by Solidus Snake, the true terrorist leader. Solidus reveals that he once adopted Raiden, a former child soldier, as his son during the Liberian civil war and that Raiden is now a Patriot agent. Olga, working as a Patriot double-agent within the Sons of Liberty, helps Raiden escape, and he locates Snake within Arsenal Gear. As they fight through the mammoth vessel, Raiden's commanding officer begins to act extremely erratically, often speaking complete nonsense. It becomes apparent that the "Colonel" that Raiden has been taking orders from is actually a creation of the GW super-computer, pieced together from information about Colonel Roy Campbell coupled with Raiden's own expectations in order to manipulate him. The erratic behavior of the simulation is the result of the virus uploaded earlier beginning to damage GW's systems.

With Snake holding off a vengeful Fortune, Raiden is forced into battle with the 25 Metal Gear RAY units guarding the Big Shell. Olga intervenes to protect him, but is restrained by one of Solidus' robotic tentacles. Olga explains that two years ago, right after giving birth to her child, the Patriots took her away and have been holding her child hostage ever since. Olga continues to explain that the Patriots blackmailed her, ordering her to become a double-agent and make the S3 plan a success or her child would be killed. After explaining, Solidus shoots Olga in the head and throws her corpse out of the way. The RAY units begin to malfunction, attacking each other and Solidus as the virus tears through the GW AI's program. Arsenal begins an emergency ascent, and Snake, restrained by Fortune, Solidus, and Raiden are carried to the roof of the fortress as it surfaces. To Solidus' increasing rage, Ocelot reveals that he too is a Patriot agent, the entire episode was a carefully coordinated attempt to reenact the events of the Shadow Moses incident; what Ocelot describes as the 'S3 Plan', or Solid Snake Simulation, designed to turn Raiden into the perfect soldier. He kills Fortune and boards the prototype Metal Gear RAY stolen from the tanker two years previously, and attempts to finish off the survivors of the exercise. However, Liquid possesses him, and announces his plan to hunt down the Patriots based on his host's knowledge. Setting Arsenal on a collision-course with New York, Liquid-Ocelot launches RAY into the ocean, followed by Snake.

Arsenal comes to a halt in downtown New York, launching Raiden and Solidus onto the roof of Federal Hall. Solidus reveals to Raiden his reasons for trying to steal Arsenal: a nuclear electro-magnetic pulse would take down Manhattan's digital infrastructure and allow Solidus to lead it as a republic against the Patriots, a nation of "Sons of Liberty". Likewise the Patriots, via another AI, contact Raiden to reveal the truth of their actions, the AIs being programmed to becoming "digital censors", removing trite and needless information from the electronic world in what they call "Selection for Societal Sanity", or "S3 Plan". The information fed to Ocelot was another part of this plan. However, with such a control over the flow of digital information, they could as easily be manipulating perceived history for the Patriot's needs. Believing the only option available is to track down the Patriots using the information in Raiden's neural implants, Solidus offers his son one final duel.

Raiden defeats Solidus, and as crowds descend upon the wreckage of Arsenal Gear, Snake and Raiden meet one last time, where his mentor informs him that only he can choose what to believe in, and that he must pass on what he believes to be true. Having planted a tracking device on Liquid-Ocelot's Metal Gear, he and Otacon plan to follow him, and to hunt down the Patriots, whose details were hidden in the GW computer virus disc. As Snake disappears into the crowd, Raiden is finally reunited with Rose, on April 30, 2009—the 220th anniversary of George Washington's inauguration as President of the United States, and the anniversary of Rose and Raiden's first meeting.

In a brief epilogue, Otacon and Snake discuss the decoding of the virus disc, which contains the personal data on all twelve members of the Wisemen's Committee (the Patriots' high council). It is revealed on this disc that one of the members of the committee was a major sponsor of Philanthropy. Another shocking revelation found on the disc indicates that not only are all twelve members of the Wisemen's Committee dead, but have been dead for approximately 100 years.

Metal Gear Solid 4: Guns Of The Patriots
Set in 2014, five years after the "Big Shell Incident" (the events of the Plant Chapter from Metal Gear Solid 2), Metal Gear Solid 4 portrays a world where the restriction of military intervention on foreign soil has been eased, fueling the need for private military companies (PMCs) to fight proxy wars for business purposes. Nanotechnology has become prominent, both to enhance the capabilities and enforce the loyalty of mercenaries. The nanomachine system that PMCs use is called "Sons of the Patriots" or "SOP". The five largest of these PMCs (Praying Mantis, Otselotovaya Khvatka, Werewolf, Pieuvre Armement and Raven Sword) are owned by a single mother company named Outer Heaven, operated by Liquid Ocelot. Amassing an army whose manpower rivals that of the United States, Liquid prepares to launch an armed insurrection by taking control of SOP. With the world once again in crisis, a rapidly aging and disillusioned Solid Snake is deployed into the Middle East by Roy Campbell to terminate Liquid. Guns of the Patriots takes place in five locations: the Middle East, South America, Eastern Europe, Shadow Moses Island, and Outer Haven.

Act 1 - Liquid Sun

Snake begins his mission by infiltrating a war-torn Middle Eastern city with a local militia convoy. The militia is locked in conflict with troops from Praying Mantis, one of Liquid's PMCs. After the convoy is decimated by Praying Mantis troops and Gekko units, Snake meets up with Metal Gear Mk. II, a robotic drone Otacon developed to assist him remotely, and receives orders to meet up with Campbell's informants, Rat Patrol Team 01. On the way to the rendezvous point, Snake encounters Drebin 893, a "gun launderer" who can unlock ID-locked weapons found on the battlefield. Drebin agrees to launder the ID-locked weapons Snake obtains as long as Snake provides him with the extra firearms he acquires. After leaving Drebin, Snake meets up with Rat Patrol in the abandoned Advent Palace hotel and is shocked to learn that Meryl Silverburgh is the leader of the team. After Snake and Meryl discuss their assignments and pasts, Advent Palace is raided by Liquid's elite soldiers, the FROGs. Rat Patrol, with Snake's help, escapes the building. Snake continues towards the main Praying Mantis camp, where Liquid was last sighted, and prepares to assassinate him. Before he can carry out his objective, an unknown force causes all of the soldiers in the area to collapse in pain and begin violently attacking each other. The nearby members of Rat Patrol are also affected. As Liquid escapes in his helicopter, Snake also collapses, but as his vision fades, he is given a syringe by Dr. Naomi Hunter and is carried away to safety by Johnny Sasaki, the lone unaffected member of Meryl's team.

Act 2 - Solid Sun

Following Snake's rescue, Otacon receives an encoded message from Naomi, which explains that she is being held captive in South America. Snake plans to take advantage of a rebel uprising in the area to sneak into the base of Pieuvre Armement, another of Liquid's PMCs, where Naomi is being held. Snake infiltrates the area and meets up with Drebin, who reveals that The Patriots are actually a network of five AIs. Four AIs are named after US Presidents: GW, TJ, TR and AL. These are controlled and regulated by the 5th AI named JD (John Doe), the core AI. After Snake finds Naomi, she explains that Liquid is planning to use Big Boss's genetic information to access JD and take control of SOP (Sons of the Patriots), the system of nanomachines and ID-authentifications which allow the Patriots to monitor and control soldiers. She also explains that Snake's aging is due to intentional gene manipulation of Big Boss's clones, and that he will have a shortened lifespan. However, his shortened lifespan is less of a concern to Naomi than the fact that the FOXDIE virus in Snake's body has begun to mutate. She estimates that in 3 months the virus will have become mutated enough to attack anyone, not just the people it was programmed to target; he has become "a walking biological weapon". After Snake defeats Beauty and the Beast Corps. member Laughing Octopus, Snake and Naomi escape with Drebin, defended by Raiden, who mysteriously resurfaces as a Cyborg Ninja after disappearing for several years. Raiden holds off numerous Gekkos and a resurrected Vamp while Otacon rescues Snake and Naomi via helicopter, but is seriously wounded in the process. Raiden leaps onto the helicopter but soon loses consciousness; before he blacks out, he briefly mentions that a Dr. Madnar in Eastern Europe can help him.

Act 3 - Third Sun

On the Nomad, Naomi explains that Big Boss is in fact alive, although brain dead. His body is in the control of the resistance group Paradise Lost in Eastern Europe. While Snake locates the group, Naomi and Sunny take Raiden to get his required dialysis from Dr. Madnar. By stalking a Paradise Lost member Snake manages to find their leader, Big Mama, who reveals herself to be EVA, the surrogate mother of Solid and Liquid and former lover of Big Boss. She reveals the origins of the Patriots, founded by Major Zero forty years ago. An army led by Raging Raven suddenly attacks the group's hideout, and Snake and Mama escape on a motorcycle, along with decoy vans to keep the attackers from finding Big Boss's body. At the end of the chase, the motorcycle crashes, and Mama is wounded. Snake is attacked by Raging Raven, and is forced to fight her. When Snake returns from the battle with Raven, he and Mama escape down a sewer connecting to the Volta River, where Liquid is waiting for them, and displays his power over SOP by incapacitating an entire army of American troops mentally, through his ability to lock down the system controlling their nanomachines. He incinerates Big Boss, and Big Mama is severely burned attempting to rescue him. The left side of Snake's face is badly burned as he rescues her from the flames. As Liquid makes his escape in a gunboat down the river, Big Mama dies in Snake's arms.

Act 4 - Twin Suns

Liquid's final plan is to destroy JD, the Patriot's core AI, so that he may seize control of the Patriots' network with GW, which Liquid apparently repaired and took control of shortly after the Manhattan incident. To this end, Liquid plans to use the only WMDs not still controlled by the Patriots: the stealth warheads launched by Metal Gear REX's rail gun, to fire a nuclear warhead at JD, which is housed within a satellite disguised as orbital debris. Snake returns to Shadow Moses Island, where REX has remained in the nine years after the events of Metal Gear Solid, to stop Liquid from stealing it. After defeating Crying Wolf and a squadron of FROGs, Snake approached Metal Gear REX to find that its Rail Gun has been removed. In the hangar, Snake is attacked by Vamp until the timely arrival of Raiden. Snake fights off a unit of self-destructing Gekko while Raiden finally defeats and kills Vamp, after Snake suppresses the nanomachines which give Vamp his apparent immortality. Naomi then appears and ends her life by suppressing her own nanomachines, allowing her cancer to kill her. Otacon manages to reactivate REX, and Snake and Raiden pilot it to escape to the harbour. Raiden, defending from the rear, becomes trapped under some rubble, while Snake uses REX to fight Metal Gear RAY piloted by Liquid. After the fight Liquid reveals his ultimate weapon: a battleship based on stolen Arsenal Gear prototype blueprints, named "Outer Haven", with REX's Rail Gun mounted on it. Liquid tries to crush the crippled Snake by ramming Haven into the dockside, but Raiden cuts off his own arm to escape the rubble and is able to restrain the ship temporarily, allowing Snake to escape with his life.

Act 5 - Old Sun

Aboard the re-commissioned battleship USS Missouri, Mei Ling plans to catch up with Outer Haven, which needs to wait until it is as physically close to JD's satellite as possible in order to get the most precise shot from the Rail Gun. A strike team consisting of Snake, Meryl and Johnny is created in order to infiltrate GW's physical processor and upload a computer virus that will destroy the AI. Infiltrating the vessel, Snake defeats Screaming Mantis, who is revealed to have the implanted personality of Psycho Mantis. Snake is forced to leave Meryl, Johnny, and Raiden behind to hold off FROG units while he approaches GW through a corridor lined with microwave emitters which nearly burn him alive. Though Snake is severely weakened by the heat exposure and overwhelmed by Outer Haven security drones, the Mk. III manages to upload the virus. The virus unexpectedly uses GW as a conduit to infect the whole AI network, destroying all five Patriot AIs, disabling SOP and all military systems implementing it worldwide, including Liquid's, saving the lives of Raiden, Meryl, Akiba and all personnel aboard the Missouri who were under attack from Outer Haven. A video recording of Naomi set to play back after the destruction of the Patriots explains to Snake and Otacon that SOP was just the beginning of the Patriot's plans, and that they had intended to implement nanomachine personality control worldwide. She goes on to explain that she and Sunny designed the virus as the antithesis to FOXDIE; as the nanomachines used in SOP were technological derivatives of Naomi's FOXDIE, the new virus would atone for Naomi's mistake by shutting down the nanomachine system. For this reason, the new virus was named 'FOXALIVE'. Sunny's programming also made sure that in destroying the Patriot AIs, SOP and the War Economy, FOXALIVE would preserve the systems controlling vital and benign world infrastructures such as water, air, telecommunications and the internet.

The U.S. Marines easily take over the now-defenseless Outer Haven, its unmanned units deactivated and its soldiers in a state of withdrawal from the SOP nanomachines. In the confusion, Liquid takes Snake to the sail of Outer Haven and thanks him for accomplishing Liquid's own goals. His plan to use REX's rail gun was just a diversion so that Snake's own attempts to bring down the system would go unnoticed by the Patriots, who had anticipated Snake protecting them by stopping Liquid. Ocelot had allowed the will of Liquid to live on within his body through the use of hypnosis and auto-suggestion, perpetuating both Liquid's own agenda against the Patriots, as well as the feud between the two sons of Big Boss. Ocelot allowed Liquid's personality to carry out it's plan against the Patriots, knowing that JD would be allocating its resources into stopping Liquid and not into preventing the upload of FOXALIVE. After this revelation, Liquid's personality declares that they have 'a score to settle', and acts upon his final wish within Ocelot's body for the sons of Big Boss engage in one final unarmed fight on top of Outer Haven. As Snake and Liquid wage their brutal fist fight, Ocelot's personality gradually resurfaces, culminating in the use of his trademark hand gestures. His last words are "You're pretty good...", echoing his taunts against both Solid Snake and Big Boss during the events of Metal Gear Solid and Metal Gear Solid 3: Snake Eater.

Epilogue - Naked Sin

In the epilogue, Meryl and Akiba get married. Their wedding, held on an airfield, is attended by the members of Rat Patrol, Otacon, Sunny, Drebin, Mei Ling and Campbell. Meryl reconciles with Campbell. Raiden's body is reconstructed and made to look normal, and he reunites with his fiancée Rose and their son, which Rose has lied about miscarrying. Rose reveals that her marriage to Roy Campbell was a charade to keep her protected from the Patriots during the course of Raiden's mission. Sunny gives away the Mark III to a local boy, and asks Otacon where Snake is, to which Otacon replies that he has taken a trip. His last line to Sunny is "Snake had a hard life", before flashing to the next scene. Snake attempts to commit suicide by gunshot in the graveyard housing the graves of Big Boss and The Boss in order to prevent his mutated FoxDie strain from spreading further, stating that killing himself is his "final mission." Drebin reveals to Otacon he was a child soldier who was adopted by the Patriots with the intention of raising him to become a gun launderer. He also explains that Rat Patrol 01 (RAT PT 01) is an anagram of PATR10T, showing that the Patriots had been manipulating Meryl's team from behind the scenes as well.

Debriefing - Naked Son

Back at the cemetery, it is revealed that Snake fired the gun in another direction, and didn't kill himself. A familiar voice approaches Snake and encourages him not to kill himself. Snake turns in disbelief to find Big Boss standing before him. Big Boss tells Snake that the body burned on the Volta was actually that of Solidus, and that he was reconstructed with surgery using parts from both Solidus and Liquid's bodies, and kept alive with intensive nanomachine technology similar to that used to restrain members of the B&B Corps. He brings Major Zero along with him, now elderly and confined to a wheelchair in a vegetative state.

Big Boss explains that Zero created the Patriots as an interpretation of The Boss' will, along with Eva, Ocelot, Sigint, Para-Medic and Big Boss himself. As the Patriots became more and more influential in society, Zero became a megalomaniac, obsessed with uniformity and erasing individuality, leading Big Boss to become disaffected enough to leave the Patriots and form Outer Heaven as another interpretation of The Boss' will. Big Boss was followed out of the Patriots by EVA and Ocelot, who joined him in his struggle to end the Patriots. As Zero became elderly, control of the Patriots was increasingly left in the hands of JD and the proxy AIs, who further misinterpreted Zero's will and completely alienated themselves from the original will of The Boss. JD sought ways to control the masses through manipulation of the economy, (which lead to the War Economy), digital information (which lead to the creation of Arsenal Gear) and eventually personalities (which became the SOP system). He goes on to explain that Ocelot willingly used hypnosis, nanomachines and psychotherapy to assimilate the personality of Liquid Snake, in order to fool the system and propagate the feud between the sons of Big Boss. He takes it upon himself to "send Zero back to nothing", and euthanizes Zero by turning off his life support.

Big Boss reveals that the injection given to Snake by Drebin in Act 1 included a new strain of FOXDIE, created by the proxy AIs in order to kill the surviving defectors of the Patriots, explaining the deaths of EVA and Ocelot. Big Boss also relays Naomi's message that the new FOXDIE strain has neutralized the older strain, meaning that Snake is no longer in danger of becoming a biological weapon. After telling Snake this, Big Boss also reveals that the newer FOXDIE is already affecting him, and that he, Big Boss, is being attacked one last time by the Patriots through Snake. He finally makes peace with Snake before dying on The Boss' gravestone, his last words being: "This is good... Isn't it?"

In the post-credits scene, Snake explains to Otacon that he will spend his remaining days attempting to simply live his life (and has also quit smoking). Otacon wishes to come with him in order to chronicle the last days of Solid Snake. Snake initially refuses but with some persuasion ultimately relents, allowing Otacon and Sunny to accompany him.

 

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