Snake proves more than adequate, though. Making contact with a local resistance, headed by a Kyle Schneider, he manages to rescue Gray Fox and the Russian robotics engineer Doctor Drago Madnar, the latter being responsible for the creation of the Metal Gear prototype. Fox reveals that "Metal Gear" is a Humongous Mecha that can dominate conventional battlefields and launch nukes; on its back, Outer Heaven intends to establish itself as the world's only superpower. Snake sets out to destroy it, but soon discovers that the traps in his way are tuned perfectly to him. Additionally, Big Boss, who has been supporting him via radio, begins to deliberately mislead him, up to and including establishing the series' love of Breaking the Fourth Wall by demanding the player turn off their console. After Snake destroys the Metal Gear, all is revealed: Big Boss is, himself, the founder of Outer Heaven. He and Snake engage in hand-to-hand combat, having already engaged the base's self-destruct; but Snake defeats him and lives to fight another day.
Landing in Zanzibarland, Snake comes across Holly White, a CIA operative posing as a freelance journalist, and Gustava Heffner, an agent for the Czech State Security and Dr. Marv's bodyguard, who both assists him in his mission.
Along the way, Snake also makes a disturbing discovery when he is confronted by one of Big Boss' top people, the so-called "Black Ninja". Upon defeating Black Ninja in battle, Snake discovers that his true identity is that of Kyle Schneider, the former leader of the resistance against Outer Heaven. Heavily wounded, Schneider explains that the NATO bombed Outer Heaven indiscriminately after Snake completed his mission, killing and injuring many members of the resistance in the process and devastating the area. When Big Boss showed up again following the bombing campaign, and provided aid to everyone affected by it, Schneider changed his outlook on the man and instead came to support his cause. After a stint in as an operative in NASA's top-secret Extraterrestrial Environment Special Forces Unit, where he was outfitted with an experimental flex armor and reflex-enhancing drugs, Schneider came to Zanzibarland to join Big Boss on more permanent basis. With his last breath, he gives Snake a hint about where to find Dr. Marv, hinting that is what Big Boss wanted.
Instead of finding Dr. Marv at the hinted location though, Snake runs into yet another familiar face, that of Dr. Madnar, who explains that Big Boss had him abducted again, and is now forcing him to work on the Metal Gear D. He is, however, able to provide Snake with Dr. Marv's new location, allowing Snake to finally find the scientist though it turns out that is unable to understand him, as he can only speak Czech and Slovak. Snake joins up with Dr. Madnar, who suggest that they try to seek out the assistance of Gustava to translate for Dr. Marv.
As Snake, Gustava, and Dr. Madnar head toward Zanzibarland's main prison, Gustava is mortally wounded by a missile fired by Metal Gear D, the pilot of which is revealed to be none other than Gray Fox, and Dr. Madnar is recaptured by the enemy. Gustava dies in Snake's arms, but not before giving him the key to the locker where Dr. Marv has hidden the formula for OILIX inside a MSX cartidge.
Snake is able to find Dr. Madnar again, along with the body of Dr. Marv. Dr. Madnar explains that Dr. Marv was tortured for information, and that his heart couldn't take the stress of it. Holly contacts Snake, revealing to him that Dr. Madnar is likely a traitor. Being suspicious of him, she asked the CIA to run a check on his background, finding out that his colleagues in the scientific community in the US had ostracized him for his radical ideas, and that he had voluntarily come to Zanzibarland to oversee the development of the new Metal Gear. With the truth out, Dr. Madnar confesses that angry over being rejected by the US, he deflected to Big Boss' side to seek his revenge, and he admits that he was responsible for the ambush that lead to the death of Gustava as well as accidentally killing Dr. Marv. He then attacks Snake, forcing the soldier to violently incapacitate him.
Snake goes on to confront Gray Fox in the Metal Gear D, and manages to destroy the mech after a fierce battle. Unfortunately, the resulting explosion causes Snake to catch on fire, making him lose most of his gear, while Fox, though injured, is able to steal the OILIX formula from Snake while he was distracted. Snake chases Fox into a minefield, where the renegade challenges him to a fist fight. After an extended fight, Snake emerges victorious, while Fox, exhausted and bleeding out from his wounds, tells Snake about his past, detailing how his life was saved by Big Boss more than once, but in the end that was not the reason why he joined up with him. That decision happened after he felt his shot at a normal life had failed when a romantic relationship turned sour — it turns Gustava was his lover — and he came to believe that could only find his purpose in battle, despite professing a hatred for war itself. Snake offers Fox some reassuring words as he (apparently) expiries, promising him that he will be reunited with Gustava on the other side. Snake then recovers the OILIX formula from his body.
Just then, Snake hears a familiar voice taunting him over the base's PA system. Following the voice into a storage room, Snake once again finds himself face-to-face with the legendary Big Boss. Snake declares that he has come here to Zanzibarland to get rid of the nightmares that he has endured since Outer Heaven. Big Boss tells him, earnestly, that they probably will never go away, before bridging into his Motive Rant, saying that once a soldier has experienced the taste of battle, they will never able to let go of it, and are unable to lead normal lives as they will always hunger for their next battle until they die, revealing that this was his reason for creating Outer Heaven and now Zanzibarland. He wishes to create a world order that is capable of creating perpetual conflicts and wars, so that there will always be new battlefields to send soldiers out to fight and die in. Snake declares that he is still determined to fight and stop him, and Big Boss obliges his wish. Though having lost most of his gear, Snake is still able to improvise a makeshift flamethrower by using his cigarette lighter and a lacquer spray he finds in the storage room. Taking Big Boss by surprise, Snake is able to defeat him, for the second and last time.
Snake is able to meet up with Holly again, and shooting their way out, the two of them manage to make their escape via helicopter. In the aftermath, Campbell offers Snake to rejoin FOXHOUND on a more permanent basis, but Snake rejects this.
This time it's FOXHOUND itself that has gone rogue: all six members — Vulcan Raven, Sniper Wolf, Revolver Ocelot, Decoy Octopus, Psycho Mantis, and Liquid Snake — have taken over Shadow Moses Island in the Alaskan archipelago, occupying it with the help of the Next-Gen Special Forces, soldiers who have undergone gene therapy. This seemingly unimportant dot of land is anything but: not only is it a nuclear weapons disposal facility, where warheads are dismantled, but it's also the place where DARPA is working with the (fictional) company ArmsTech to develop yet another Metal Gear, this one codenamed REX. Designed by Hal "Otacon" Emmerich, REX uses a railgun instead of ballistic missiles to deploy its warheads, which would fool conventional anti-missile systems that typically use a ballistic missile's exhaust plume for target-seeking purposes. (This is called a "stealth" warhead in-game, but the physics of such a claim might not hold up.)
Solid Snake is rousted out of retirement once again, with Campbell and Miller on the radio to advise him. His two objectives: determine if the terrorists actually can launch a nuke; and, if they can, make sure they don't. He is sent into Shadow Moses with the clothes on his back, a pack of cigarettes he swallowed after mission doctor Naomi Hunter gave him an injection that suppresses his stomach acids, and nothing else. Of course, "the clothes on his back" are not nothing either: they contain his "CODEC" radio system with which he can remain in constant contact with his support team, as well as a "Soliton Radar" developed by tech genius Mei Ling that allows him to see enemy soldiers and predict their fields of view. Using these tools, he is able to begin gathering weapons, information and allies.
Snake makes contact with a number of people imprisoned on the base by the terrorists: DARPA head Donald Anderson, ArmsTech President Kenneth Baker, Otacon, and Meryl Silverburgh, a soldier who happens to be Campbell's niece. The four of them help Snake determine that, yes, the terrorists can launch a nuclear weapon. Otacon and Meryl go on to support Snake on-site, but both Anderson and Baker suffer fatal heart attacks just after speaking to Snake. Snake also faces three members of FOXHOUND: Vulcan Raven, who attacks from the safety of a tank; Revolver Ocelot, whose duel with Snake is cut short when a cyborg ninja pops in and slices off his arm; Sniper Wolf, who attacks from long range; and Psycho Mantis, who takes Breaking the Fourth Wall to an entirely new level by using Interface Screw tactics, such as making the player believe their PlayStation has accidentally turned off, using its vibration mode to shake the controller, and refusing to be hit until the player plugs their controller into the second controller port. Snake is also required to fight the cyborg ninja. He realizes the ninja is none other than Gray Fox, resulting in confusion and horror from Naomi.
After a series of adventures, misadventures and Boss Fights, Meryl and Snake are taken prisoner. Snake is stripped naked and strapped to a torture bed, where he finally meets Liquid Snake, who claims to be Snake's twin (despite the fact that he is blond while Snake has brown hair). Ocelot also reveals that Snake never met Donald Anderson: the real one was killed during an overenthusiastic infusion of torture by Ocelot, and Decoy Octopus took his place (and died of the heart attack). Snake must endure a Button Mashing minigame to resist Ocelot's electrocutions; he can surrender, but Ocelot promises that if he does, he (Ocelot) will kill Meryl.
Fortunately, Otacon remains at large, courtesy of his Invisibility Cloak. He helps Snake escape, and Snake uses keycards to flip the launch failsafe on Metal Gear REX, rendering the weapon system unable to launch a nuke. Unfortunately, it turns out that he was duped into doing so by Decoy Anderson, and has actually disabled the failsafe. Additional treachery is discovered: Naomi reveals that she was ordered to infect Snake with a nanomachine virus, "FoxDie," that will inflict "heart attacks" on every FOXHOUND member currently on Shadow Moses — which, of course, includes Snake himself. She has done this partially out of revenge, as her adoptive brother, Frank Jaeger, is Gray Fox. (She also helped stage Frank's escape from the lab of the treacherous cyberneticist Dr. Clark, who was slain in the chaos.) Campbell also informs him that Miller's corpse has been found, dead for at least three days. The "Miller" on CODEC reveals himself to be Liquid Snake. Liquid reveals that he and Snake are both clones of Big Boss, created by the "Les Enfants Terrible" project; he resents Snake because some genetic modification occurred, and he (Liquid) got the bad end of the stick, being stuck with all the recessive genes while Snake got all the dominant ones. This is not how genetics works, but that doesn't stop Liquid, who jumps into REX and begins to attempt to squish Snake to death. However, Snake is able to defeat it, with assistance from Gray Fox, who sacrifices himself to Attack Its Weak Point, allowing Snake to deliver the final blow to the massive robot. The two Snakes then fistfight atop the wreckage of REX, with Meryl's motionless body hanging in the balance.
Snake escapes with Otacon (if he lost the torture minigame; Meryl is discovered to be dead) or Meryl (if he won; Otacon stays behind to safeguard the way out). They are pursued by Liquid, who refuses to go down regardless of the punishment dealt him; only FoxDie itself is finally able to stop him. Naomi admits that she has no idea when FoxDie will kill Snake himself, so Snake decides to live out the rest of his life as best he can. Meanwhile, Ocelot makes a telephone call to his superior and confirms that he managed to escape with the design data for Metal Gear REX. He works for a fellow named George Sears, who happens to be the third Les Enfantes Terribles clone, not to mention the 43rd and current President of the United States.
Act 1 - Tanker ChapterIts first half takes place in 2007. In the intervening years, Ocelot has gone public with the Metal Gear REX plans, selling them to anyone who wants them, and by now many nations are armed with home-made REXes. It's unknown what President Sears thinks about this because his term is over. Snake and Otacon are not happy about it; they've formed a non-government organization, Philanthropy, to combat the proliferation of Metal Gears. The USMC are not happy either; they've developed a counter-weapon, the amphibious Metal Gear RAY, and are ferrying it into the New York Harbor on an oil tanker, the USS Discovery. This particular development has put the two of them at odds, and as the tanker passes under the Verrazano-Narrows Bridge, Snake jumps off the bridge and boards it. His objective is to get photographic evidence of RAY.
Of course, things are more complicated than they seem. First off, the tanker is already being subjected to hostile action: a group of Russian mercenaries, led by Col. Sergei Gurlukovich and his pregnant daughter Olga, are boarding it. Second, as Marine commander Scott Dolph musters his remaining men and makes a grand speech about the peacekeeping abilities of RAY, they are ambushed both by Gurlukovich and then by his associate — Revolver Ocelot. Ocelot becomes the Trope Namer for Chronic Backstabbing Disorder by betraying both Dolph and Gurlukovich, but is then backstabbed himself by, of all things, his arm, which was actually transplanted from the corpse of Liquid Snake. After taunting Snake, Liquid Arm-celot makes off with RAY, leaving the Discovery sinking into the harbor and Snake adrift in the water.
Act 2 - Plant ChapterIt's 2009. The sinking of the Discovery in the New York Harbor has caused a major ecological crisis, and a clean-up facility, the "Big Shell," has been built on the water. It has been seized by a terrorist group, the eponymous Sons of Liberty, whose leader claims to be Solid Snake; they are aided by "Dead Cell," a group of American soldiers who pretended to be terrorists in order to test the security of military installations, and now have decided that Becoming the Mask is a good idea. The members of Dead Cell include Fatman, an explosives expert on roller skates; Vamp, who can walk on water and doesn't seem to stay dead (though he can be killed, and is several times over the course of the game); and their leader, Fortune, daughter of the late Scott Dolph, who apparently can be killed but cannot be shot: bullets just kind of detour around her. The Sons of Liberty have also employed Olga Gurlukovich, no longer pregnant (it has been two years), who leads the survivors of her father's mercenaries.
Since Solid Snake is the Player Character, one would typically assume that he is not simultaneously the Big Bad... until one discovers that Solid Snake is not the Player Character. Instead, players control the New Meat from FOXHOUND: a slender, almost effeminate man named Jack, operating under the code name Raiden. (This Plot Twist was poorly received by the fanbase, and Raiden largely seen as The Scrappy.) Supporting him by CODEC are Col. Campbell and Rosemary (no last name), the data specialist who saves his game. She is also his girlfriend, and occasionally interrupts the mission to discuss their personal life, particularly Jack's spartan living quarters and daily Catapult Nightmares. (Rose also received a cool reception from the fanbase for a set of Skewed Priorities.) Raiden has, in theory, on-site support in the form of SEAL Team 10, but they are slain almost to a man by Vamp; the sole survivors are Peter Stillman, a bomb-disposal expert who mentored Fatman, and Iroquois Pliskin, a man who wears a SEAL uniform but has the same face as Solid Snake, the same voice actor as Solid Snake, and whose names are both references to snakesnote . He also gets assistance from a mysterious Cyborg Ninja. With their help, Raiden is tasked with infiltrating the Big Shell and rescuing the hostages being kept there, which include James Johnson, 44th and current President of the United States.
The first threat to be dealt with is Fatman, who has littered the struts of the Big Shell with bombs. Raiden, Pliskin and Stillman mobilize to prevent them from going off. Raiden fights and defeats Fatman, but Stillman is lost to a trap. Pliskin then proposes the plan of evacuating a number of hostages using a helicopter. Raiden agrees, despite skepticism from Campbell. However, the helicopter is attacked by a Harrier jet flown by the man who claims to be Solid Snake. Pliskin solves that dilemma once and for all by revealing that he is the true Solid Snake, and he and the pilot of the helicopter (Otacon) help Raiden shoot the Harrier down. However, it is rescued by the Metal Gear RAY which Ocelot stole two years ago.
Raiden, now with Otacon and Snake providing advice via CODEC, reaches President Johnson, who lives up to his name by performing a Crotch-Grab Sex Check. Johnson reveals that the Big Shell is actually a cover-up for a larger construction project: the next Metal Gear. A giant submarine called "Arsenal Gear," it houses an AI, "GW," which is intended to control the transmission of all digital information. He also reveals that he, his predecessor George Sears, and most presidents through the 70s have all been Puppet Kings, manipulated by an Omniscient Council of Vagueness called "The Patriots" who secretly control not just America but most of the world. They are so secretive that people under their control can't even say "The Patriots"; instead, they are forced to proclaim "The La-Li-Lu-Le-Lo." (This sounds, and is, a little silly, but keep in mind that due to the nuances of Japanese Ranguage, it is impossible to specify that the speaker should use the L consonant instead of an R. In this way, the Patriots—excuse me, the La-Li-Lu-Le-Lo—have rendered their name not only unspeakable but unwriteable too.) Sears, the President explains, got fed up with the situation and decided to rebel, taking on the name "Solidus Snake" and becoming the leader of the Sons of Liberty — the man flying the airplane Raiden just shot down. Solidus, in addition to being one of Les Enfants Terribles, is an unmodified clone of Big Boss, which is more than either Solid or Liquid could say. Having received this Info Dump, Raiden attempts to lead the President out of danger, but instead Ocelot shows up and blows him away. He then leaves Raiden alone.
Raiden is now directed to stop Arsenal Gear by any means possible. He travels deeper into Big Shell to reach its primary designer, E.E. — Emma Emmerich, step-sister of Otacon. They haven't spoken for a while, not since his father (her stepfather) committed suicide. She is also deathly afraid of both insects and water, which is bad because Raiden had to swim through bug-infested flooded corridors to get to her. Nonetheless, Raiden succeeds in bringing her to the outer area of the Big Shell ("Colonel, we've managed to avoid drowning!"), where she agrees to upload a virus into Arsenal Gear's mainframe. He protects her with a sniper rifle fire while she crosses to the main control center... only for Vamp to pop up and put a knife through her. She admits to Otacon that she kind of had a thing for him; Otacon then admits (to her corpse) that he was doing his stepmother, which is part of why his father killed himself. (The Emmerichs are a weird family.) In any case, Otacon uploads the virus, and then evacuates the remaining hostages on his chopper while Snake and Raiden prepare to invade Arsenal Gear. ...Only, the Cyborg Ninja, revealed to be Olga Gurlukovich, aids Snake in incapacitating Raiden and turning him over to the remaining triumvirate of villains—Solidus, Fortune and Ocelot.
This is about the time when the game starts getting extremely weird, to the point that we actually have an entire article dedicated to analyzing it.
Raiden wakes up in a torture chamber that is almost identical to the one Snake was in on Shadow Moses. His assailant is different, however. Solidus reveals that Raiden once served him as a Child Soldier during the Liberian Civil War, and condemns him as a pawn of the Patriots. After Solidus leaves, Olga springs Raiden from imprisonment. It turns out that her daughter was kidnapped by the Patriots when she was born—almost literally snatched out of Olga's arms—and they are threatening to kill the child if she (Olga) doesn't cooperate. The only problem is, Snake has all of Raiden's gear, meaning Raiden needs to sneak naked (literally — his character model had to be designed with Barbie Doll Anatomy in case anyone managed to get a look) through the bowels (literally — the level area is marked "duodenum," which is part of the large intestine) of Arsenal Gear to reach him. Even worse, Col. Campbell has started to go batshit crazy, spewing Word Salad Lyrics and insisting that Raiden turn off the PlayStation 2 so that he (Campbell) can take over and fix all of Raiden's mistakes. Otacon discovers that it's not even Campbell: it's a construct created by GW, which is why Emma's virus is driving it ("Campbell") insane. Rosemary also reveals heretofore undetected treachery: she admits that she is an agent sent by the Patriots to seduce Raiden, one who Fell In Love with the Mark. She also, just before the connection shorts out, claims to be pregnant with his child. With all of this raining down on him, Raiden's Sanity Meter is at an all-time low by the time Snake gets to him.
Fortunately, Snake starts with an apology: his "betrayal" of Raiden was to use him as a Trojan Prisoner, allowing the three of them to infiltrate Arsenal Gear. He returns Raiden's equipment to him, including a new gift: the high-frequency Vibroweapon which Olga has wielded hitherto. Suitably armed, the two fight their way through Arsenal Gear side-by-side (in which Snake's performance is dictated largely by the difficulty setting chosen by the player) and are eventually cornered by Fortune. Snake holds her off whilst Raiden keeps after Solidus, fighting through a literal army of AI-controlled RAYs to reach him. It's all for naught, and both are captured; even worse, Olga is slain trying to defend them.
With two good guys against three Big Bads, the odds look grim... but almost immediately, Chronic Backstabbing Disorder sets in, and everyone starts squabbling. It starts when Solidus declares his intention to dig the identities of the Patriots out of GW; Fortune is to provide a distraction by using one of Arsenal's hydrogen bombs on Manhattan. Ocelot reveals that he can't allow that to happen, as he himself is an agent of the Patriots. The entire Big Shell Incident has been part of the S3, the "Solid Snake Simulation," and its parallels to the first game (Cyborg Ninja; Raiden's relationship with Solidus; renegade Special Forces unit; etc) were intentionally crafted test the hypothesis that, if you throw a soldier into the kind of crucible Snake faced on Shadow Moses (and the soldier survives), he'll come out of it a Super Soldier on par with Solid Snake. The entire exercise has been, for all intents and purposes, a Murder Simulator played straight... and, because of the way Ocelot phrases all of this, it's impossible to tell whether the subject of the Solid Snake Simulation was Raiden, the Player Character, or you, the player. This was intentional. (Note that, per Word of God, the theme of the Metal Gear series is, "It sucks to be an action hero.")
In any case, Ocelot proves that the Patriots are in charge of everything by shooting the unshootable Fortune, having disabled the Applied Phlebotinum that kept her safe. He then jumps into the original RAY to make his escape... until, once again, Liquid Arm speaks up. Furious at his brothers, he launches RAY's armaments at Snake, Solidus and Raiden... who are, miraculously, protected by Fortune, using her powers (yes, despite the disabled Phlebotinum) one last time before she leaves to join her family. Ocelot, disgruntled, decides to simply flee; Snake jumps into the ocean after him, leaving Solidus and Raiden alone atop Arsenal Gear. And, finally, the Metal Gear itself gets into the picture: with GW going insane, Arsenal Gear sets course for downtown Manhattan and careens into the city, dumping the two of them unceremoniously atop Federal Hall.
Solidus admits that Jack was orphaned because, during the Liberian Civil War, Solidus killed his parents. He wants to destroy the Patriots to return America (and the world) to true freedom, instead of one that is manipulated from behind the scenes. He then draws his katana and wakizashi and announces his intention to get the names of the Patriots from the nanomachines in Raiden's body, which will hold the information since he's been in contact with them. GW proves the point by contacting Raiden directly. It claims that Ocelot's description of the S3 plan was incorrect: it's actually the Selection for Societal Sanity, and its job is to filter out the useless content created by most of humanity, forcing mankind to confront uncomfortable truths instead of burying its head in the sand of political correctness. It orders Raiden to kill Solidus—his ninja sword against Solidus' samurai swords—reminding him that the lives of Rosemary and Olga's unnamed offspring hang in the balance. Raiden is not really sure that Rosemary is even real anymore—the Colonel wasn't—but since it's his life or Solidus's, he carries out his orders, putting an end to the 43rd President on the roof of the building where the very first President was inaugurated.
Solidus' hopes were not in vain, though. Snake tells Raiden that he and Otacon intend to hunt down the identities of the Patriots—though Emma's virus was intended to censor their names, this must mean that it knows what to censor. Raiden offers to go with them, but Snake points out Rosemary, awaiting him in the crowd. It is the anniversary of the day Jack first met her. Raiden wants to know what the point of it all is, and Snake points out that while he cannot choose his own past, he can choose his future. Jack's choice is Rosemary, and the two decide to make a life together while Snake slips away.
The closing phone call is from Otacon: he tells Snake that he has pieced together the names of the 12 Patriots. The problem is that they've all been dead for over a hundred years.
Chapter 1 - Virtuous MissionA man named Jack, code-named Naked Snake, is dropped into Tselinoyarsk in Russia. Jack is a former Green Beret now working for the FOX unit of the CIA. His radio support includes the leader of the unit, Major Tom; a doctor, Para-Medic; a technology and weapons specialist known as SIGINT; and his mentor, The Boss. The Boss, formerly operating under the codename The Joy, is the leader of Cobra Unit, the very first special forces group in history. Most of them have supernatural powers, but The Boss, who does not, is in charge, which tells you just how much of a Badass Normal she is. Under her leadership, the Cobras were instrumental in turning the tide of World War II, and they led the charge at Normandy Beach, amongst other things.
Snake's mission is to aid in the defection of a Russian scientist, Dr. Nikolai Stepanovich Sokolov, who has been working on a new nuclear delivery system called the "Shagohod". Snake infiltrates the facility, his only real opposition being a GRU Major named Ocelot. Snake defeats him quite handily and takes a moment to criticize Ocelot's training, identifying that his shooting techniques would flourish with a revolver in his hand. After Ocelot retires in shame, Snake escorts Sokolov away... only to encounter The Boss. She announces that she is defecting to Russia—specifically, to Yevgeny Borisovitch Volgin, a rogue GRU colonel who can expel electricity from his body. Volgin is here for the Shagohod, which he hopes to use to oust Khrushchev from power, and The Boss is here to help him. For good measure she throws in the Cobras, who abandon the nations of their birth to fight alongside her, and two Davy Crockett nuclear bazookas. She breaks Snake's arm and throws him off a bridge into the river below. Volgin recaptures Sokolov and airlifts the Shagohod prototype away, with Ocelot and The Boss by his side. And finally, just to make a bad situation worse, Volgin fires the (American) Davy Crockett nuke at the (Russian) research facility, covering up the situation and pinning the blame on The Boss.
Chapter 2 - Operation Snake EaterA week later, Snake's broken arm is healing, and he's sent out into the field again. During a heated phone call a few days ago, Khrushchev was very blunt with LBJ: the Red Army and the majority of the Soviet government believe that America was involved in the nuclear explosion. In order to placate them, prevent a retaliatory nuclear strike, and prove America's innocence, the Soviet Premier demands that Washington take responsibility for eliminating the Boss (so that she can be blamed as the cause of the whole situation) as well as Volgin, against whom Khrushchev cannot move openly due to political limitations. Major Tom, now changing his name to Major Zero out of remorse, commands the mission, with Para-Medic and SIGINT at his side; this time, Snake will have on-site support from two American defectors, codenamed ADAM and EVA, now operating as moles within Volgin's ranks on behalf of Khrushchev.
Snake, returning to Tselinoyarsk, encounters EVA, a motorcycle-riding, extremely-breasted blonde (though he's much more impressed by the customized M1911 she gives him). ADAM is nowhere to be found, but EVA, posing as Sokolov's girlfriend Tatyana, ends up being quite sufficient support. Snake fights his way through the Russian jungle, handling the members of the Cobras as he goes. Each is named after the emotion they bring into battle, and has powers to match: The Pain controls bees; The Fear is double-jointed and can move like a spider, attacking using poisoned crossbow bolts; The End, a fearsome sniper, can photosynthesize; The Fury, a disfigured cosmonaut, wields a flamethrower-slash-jetpack that runs on rocket fuel; and The Sorrow, a medium who can speak to the dead, is not fought because he died in 1962. Like every other Cobra, he landed on Normandy Beach, paying special attention to The Boss, who was pregnant at the time. She gave birth by emergency C-section, delivering a healthy baby boy, who was kidnapped by unknown forces. After the war, The Sorrow and The Boss returned to their home countries: she to America, and he to Russia. This was how the two of them ended up meeting as enemies in 1962, right here in Tselinoyarsk, ordered by their countries to slay each other. This was incredibly painful for both of them, as The Sorrow was not only The Boss's friend, but her lover, and the father of her wayward son; it is eventually revealed that he sacrificed himself to her, as someone behind the scenes—someone pulling the strings in both the USA and the USSR—claimed to have possession of their son, and was threatening to kill him (The Boy) if both The Sorrow and The Joy survived their battle. Though deceased, The Sorrow is present throughout the game as a ghost, visible at certain times through first-person view.
Snake also encounters the Ocelot unit, led by Revolver Ocelot, who has taken Snake's advice and now wields the weapon he is named after. There is a clear competition between the two men, but it's just as clear that Ocelot looks up to Snake. He also looks up to The Boss, and as the game progresses it is revealed that Ocelot is in fact her stolen son by The Sorrow, though it is unclear if either of them is aware of this fact. That doesn't stop The Boss from mothering him, but then she's Team Mom to everyone—treating EVA with respect, mourning her lost comrades, interceding on behalf of Sokolov, providing accurate but ignored warnings about Jack's progress, and even forcing Volgin to back down on occasion. And when you consider that Volgin's an Ax-Crazy, lightning-wielding sadist who is happy to nuke his own country, you figure out just how much of a Badass Normal The Boss is.
Snake makes his way to Grozny Grad, Volgin's personal fortress, along the way learning the nature of the Shagohod. Like most Metal Gears, it has a unique way of launching nuclear weapons. Specifically, it's a rocket tank, using itself as the first stage of an ICBM. Upon reaching Grozny Grad, Snake is discovered and tortured for information by Volgin. Though he ultimately escapes, he loses an eye, trying to protect EVA from Ocelot, who now suspects that she is a double agent. (During his escape, Snake wades down the river and "fights" The Sorrow, who narrates as the souls of all those Snake has killed over the course of the game come screaming at him. Depending on how effectively the player has pursued a Pacifist Run, the "opposition" may not consist of anyone except The Cobras, who will self-immolate even if defeated by tranquilizer weapons.) Snake must now get back into Grozny Grad and destroy the Shagohod.
Though Snake succeeds in sabotaging the Shagohod's hangar with C-4 set on a 30-minute timer, he is once again captured. Volgin this time goes on his Villain Monologue: he is a son of "The Philosophers," a group of very rich men from America, Russia and China who banded together during World War II in an attempt to guide the world from behind the scenes. Alas, after the war, they began to fracture, and their cache of funds, a $100-billion pool called the "Philosophers' Legacy," was split into bank accounts around the world. Volgin has now gained possession of these accounts, though America is also trying to get their hands on it. (During this rant, if the player jumps into 1st-person view, they will see The Sorrow holding up a digital clock showing how long remains until the C4 goes off.)
Volgin engages Snake in battle, first hand-to-hand and then (after Snake knocks him unconscious and escapes) aboard the Shagohod itself. Ultimately, he is felled by a bolt of lightning out of a clear blue sky. Snake and EVA retreat to Rokovoj Bereg, where an escape aircraft is hidden. However, there The Boss is waiting for them. She explains that the agent America sent after the Philosophers' Legacy is herself. She has succeeded—EVA now has the intelligence she collected. Now, The Boss declares, Snake must kill her, to complete his mission, exonerate their nation and prevent the outbreak of a deadly nuclear war. This is, of course, no easy feat, as The Boss is a pale-skinned blonde wearing a white jumpsuit in a field of white flowers, and has an assault rifle with infinite ammo. There's also bombers coming to blow the place up in 10 minutes. But Snake prevails. Finally, Snake and EVA's plane is boarded by Ocelot, but after an inconclusive fight, he admits defeat, acknowledging that the world is more interesting with Snake in it. The two trade first names (John and Adam), and Ocelot jumps out of the plane, allowing the Americans to depart.
(If you hit R1 to jump into first-person view after you kill The Boss, you can see her and The Sorrow, Together in Death, fading away.)
Snake and EVA escape to Alaska, where they share a night of tumultuous passion. But the next morning, EVA is gone, taking the data on the Philosophers' Legacy with her. She leaves only a tape recording of her confession. She is actually a triple agent working for China, with orders to obtain the Legacy for them as well as the data on the Shagohad project (the latter of which will jumpstart China's own nuclear weapons program). The Boss also told her (EVA) the truth about her mission: she was a Fake Defector, ordered to join Volgin in pursuit of the Legacy. After Volgin's nuke became a Spanner in the Works, the CIA chose the path of plausible deniability and declared her a "real" defector; her new orders from Langley were to sacrifice her own life at the hands of Snake to prove America's innocence. Thus her life, just like that of The Sorrow, was thrown away for the convenience of the nation she served. She ultimately went to her death knowing that, despite her Undying Loyalty, she would be remembered only as a Scapegoat Rewarded as a Traitor Deserves.
For his valor, Snake is awarded the Distinguished Service Cross by President Lyndon Johnson; and the CIA bestow on him the codename "Big Boss" in recognition of his triumph over the (now, clearly, lesser) Boss. But Snake disdains their praise, instead preferring to visit Arlington National Cemetery and salute the grave of the franchise's Big Good: a headstone marked only with "In memory of a Patriot, who saved the world." Trying yet failing to hold back tears, he is now irrevocably broken: he realizes that soldiers are cast aside as mere pawns and treated like dirt by their governments when they are no longer needed. His Start of Darkness as the Big Bad of the franchise's first two games has begun.
In the traditional end-of-game phone call, Ocelot confirms to the Director of the CIA that no one suspected that he, ADAM, was a triple agent the entire time, and that the Philosophers' Legacy was in fact in the hands of the CIA, as EVA actually stole a fake copy of it from Snake. However, the disc containing information on the Legacy only had details on half of the total amount of monies...
In 1970, six years after the events of Snake Eater, Naked Snake's former team, FOX unit, has broken their allegiance with the CIA and gone rogue. Snake is also targeted by the FOX unit, which has sent renegade FOX unit soldiers to capture him. The game begins with the torture and interrogation of Snake by one of the FOX members, Lieutenant Cunningham. Lt. Cunningham is trying to locate 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 are on the San Hieronymo Peninsula (a Russian transliteration of "San Jerónimo Peninsula") or "La Península de los Muertos", 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 charged for treason and that the only way for Snake to be exonerated from the charges is to find and apprehend the leader of the rebellion, Gene. To complicate matters, Gene has also convinced most of the Soviet soldiers stationed at the base to join their side by simply taking over the chain of command belonging to a Soviet unit which was secretly stationed inside the Colombian territory. In order to complete his mission, Snake must persuade enemy soldiers to join his ranks due to 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 at the Soviet Union to tarnish the CIA's reputation and to prolong the Cold War. Gene was actually aware of this plan from the beginning due to 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 finished ICBMG model afterward. After Gene is defeated he gives Snake the funds, equipment, personnel, and all other information regarding "Army's Heaven". On his return home, Snake is awarded for his actions, he then establishes FOXHOUND afterwards. Elsewhere, Ocelot kills the DCI (Director of Central Intelligence) and takes documents containing the identities of the Philosophers in an effort to "end them".
In the post-credits epilogue, Ocelot speaks with an unknown man on the phone, they are plotting to use the Legacy to fulfill their own agenda. Ocelot actually wanted the trajectory data of the nuke to point to the DCI, in order to blackmail the DCI into giving Ocelot the documents containing the true identities of the Philosophers. Ocelot agrees to join his new employer's project under the condition that Snake/Big Boss participates as well.
In the years between the Big Shell Incident and today, the Patriots have expanded their control over the world, primarily by way of nanomachines. Nanos now regulate the physical and emotional responses of all soldiers on the battlefield, through a system called "SOP" (Sons of The Patriots). This system not only gives soldiers enhanced senses, reflexes, and the ability to better coordinate in teams, but it also includes ID locks that prevent a soldier from even firing a weapon that they are not authorized to use. As an added bonus, it also suppresses all the combat stress and trauma a soldier would otherwise accrue as s/he is exposed to more battles. Private Military Contractors have become the driving military forces of the day, and a "war economy" has sprung up around the constant proxy conflicts being fought throughout the world, which in turn make up a huge percentage of the revenues for most world economies.
Chapter 1 - Liquid SunSolid Snake is only 42 years old, but already looks 70. He and Otacon have adopted Olga Gurlukovich's daughter and named her Sunny. Nonetheless, Col. Campbell hoists him out of retirement for one last campaign. Liquid Ocelot, as he now calls himself, has poised himself to take over five of the biggest PMCs and consolidate them into one. Snake is commissioned to kill him before he can do so. Since his body is deteriorating, he is outfitted with a muscle suit that augments his physique, as well as an eyepatch, the "Solid Eye," that acts as a Heads Up Display. Supported primarily by Otacon, who drives a small, Invisibility Cloaked robot called the Metal Gear Mark 2, Snake is dropped into the Middle East where Ocelot is making his play.
Snake is ordered to meet up with Rat Patrol 01, a special forces team already on the ground who have been surveilling Ocelot for months. The four-person fire team consists of Ed, sniper and radioman; Jonathan, the heavy-weapons guy; Johnny "Akiba" Sasaki, a clumsy and uncoordinated tech expert and Ascended Extra from Metal Gear Solid; and their leader, none other than Meryl Silverburgh (a pleasant surprise to players, since the presence of Otacon implied that her death was canon). Snake also encounters a gun launderer, Drebin 893, who injects him with nanomachines that will allow him to bypass ID locks and use any weapon acquired on the battlefield.
In addition to soldiers from both sides of the proxy conflict, whom Snake can both befriend or antagonize, Snake must also contend with "GEKKO," cyborg mecha which imitate animals. He is also introduced to the BB Corps, the Beauty and the Beast Unit—traumatized women who have become cyborg war machines as their only means of coping with PTSD. Each embodies a trait from one member of the Quirky Miniboss Squads of previous games: Crying Wolf combines The Sorrow's emotion, Sniper Wolf's job and Fortune's railgun; Raging Raven has Vulcan Raven's name, The Fury's emotion and Fatman's explosives; Laughing Octopus has Decoy Octopus's name, The Boss's emotion (remember, her original codename was The Joy) and Solidus's tentacles and FN P90; and Screaming Mantis has Vamp's throwing knives, The Fear and The Pain, and Psycho Mantis's name. After Snake defeats each one, Drebin will typically call over CODEC and give an Info Dump on the woman's Back Story, thanking Snake for helping her find peace. (Why Drebin cares about them is left unexplained, though their Stripperiffic costumes might have something to do with it.)
Snake reaches Ocelot's encampment with the help of Rat Patrol 01, and is surprised to find Dr. Naomi Hunter in his company. However, Snake is unable to complete the hit, as Ocelot somehow incapacitates every soldier present, including Snake. The sole immune survivor is Akiba, who gradually drags everyone to safety.
Chapter 2 - Solid SunNaomi passes a coded message to Snake, indicating that she is being compelled to perform Ocelot's research in South America and begging for rescue. Upon rendezvous, she puts Snake through a comprehensive physical examination and determines the cause of his accelerated aging: during the cloning process, the enfants terrible were deliberately programmed to exhibit Werner syndrome. She also discovers that the original FOXDIE virus, still lying dormant in his body, is beginning to decay, losing the careful targeting parameters she designed it with. She estimates that Snake has only about six months before it begins to kill indiscriminately, turning him into a walking biological weapon.
Naomi is hustled away by PMC soldiers while Snake takes on Laughing Octopus. After he recovers her, the two begin to head towards Otacon's chopper with the help of Drebin and his AFV. However, Liquid has a few too many Gekko to send, and all looks hopeless... until a cyborg ninja drops in to provide help. It's Raiden. Though he had intended to give up the soldierly life, he and Rosemary separated after she miscarried their child; she went on to marry Campbell of all people, and is actually one of Snake's CODEC contacts (along with Otacon and Campbell himself) throughout the game. Raiden, for his part, is instantly Rescued from the Scrappy Heap when he takes on several Gekko with nothing but his sword. (His character model shows a Heckler und Koch Mk. 23 Mod 0 in a thigh holster, but he never once uses it.) Then Vamp shows up, and Raiden takes on him in a tour-de-force display of acrobatics and stabbery. The battle is inconclusive, and Raiden is forced to retreat to the chopper, badly wounded.
Chapter 3 - Third SunSnake and Otacon make contact with resistance group in Eastern Europe who have the equipment to heal Raiden. They also claim to have taken custody of Big Boss's remains, which makes them a target for Liquid as he will need Big Boss's biometrics to hack into The Patriots' system. Snake sets out to infiltrate "Paradise Lost" and meet its leader, Big Mama. Meanwhile, Naomi seduces Otacon, but slips away the next morning.
When Snake meets Big Mama, he is surprised to learn that she is none other than EVA, still kicking ass and taking names. He is also surprised to learn that she is his mother: though he was conceived in a test tube, The Patriots did not have the technology to replace the human uterus, and EVA volunteered to carry both him and Liquid Snake.
As EVA's resistance group, Paradise Lost, deploys a number of vans and decoys to attempt to get Big Boss's remains out of the city, EVA herself takes to the streets on her motorcycle, with Snake riding shotgun. The opposition is led by Raging Raven, whose air forces prove to have the decisive edge. Snake shoots Raven down, but not before EVA takes a debilitating wound to the abdomen. The two limp their way to the Volta River, where Big Boss's actual corpse is waiting... but, alas, Liquid Ocelot has already found it. Even worse, he doesn't need it, having already found a backdoor into SOP. He sets Big Boss's remains alight, and Snake is burned across the face trying (unsuccessfully) to save it. Outnumbered by US Army and Marine Corps reinforcements brought in by the also-present Rat Patrol 01, Ocelot then demonstrates his mastery of SOP by disabling men, tanks, boats and even helicopters solely by shutting their nanomachines; his bodyguards massacre most of them. Akiba is once again the only person to withstand his influence. Snake cradles his mother as she apparently dies from the combination of exhaustion and the wounds she sustained. Fortunely, all of Rat Patrol survives (along with a handful of troops from the accompanying task force), and Drebin soon arrives to take Snake to safety.
Chapter 4 - Twin SunsThe nerds are having their day: besides Akiba, the only person who managed to keep his head was Otacon. He snuck the Mark II onto Liquid's boat as it sailed away down the Volta. Through it, he learns the remainder of Ocelot's plan: to destroy a satellite which contains JD, the Patriot AI in charge of everything. Its loss will cause the Number Two AI, GW, to step up—and, since Ocelot already controls it, put him in charge of the world. For this, though, he needs a weapon system that can get things into orbit but predates ID locks. The only thing that fits the criteria is the railgun aboard Metal Gear REX. Consequently, Chapter 4 is a Whole Episode Flashback to Metal Gear Solid 1, as Snake returns to Shadow Moses, the place where, for most of us, it all began (Metal Gear 1 and 2 were not released in America until being bundled in an Updated Re-release of Snake Eater), including a comment from Otacon about how Snake needs to switch to the game's second CD... Oh wait, the PlayStation 3 runs on Blu-Ray now, ha-ha, that won't be necessary.
Snake finds Vamp and Naomi at Shadow Moses, but is delayed in pursuing them by having to fight Crying Wolf in the same snowfield where he put an end to Sniper Wolf nine years earlier. He then descends into the hangar and finds REX basically where he left it. Unfortunately, its railgun is already gone. Even worse, Vamp wants a fight. Snake, having learned that Vamp's Regenerating Health comes from nanomachines, injects him with the same suppressor nanomachines he has been using to quell his own aging-related symptoms. This renders Vamp mortal again: the next time he dies, he isn't going to un-die. So Raiden pops in to finish the job. He delivers the final blow while Snake protects him, fending off flocks of Suicide GEKKO with the help of Wolf's railgun. Naomi, admitting she has cancer and is basically alive only because of nanomachines, injects herself with the same suppressors and expires on the spot, to Otacon's sorrow.
Ocelot floods the hangar with Suicide GEKKO, so Snake, Raiden and Otacon (in his replacement mini-bot, the Metal Gear Mark III), make their escape by booting up REX. Outside, though, they find Ocelot waiting... in RAY. It's the fight every player never realized they wanted: REX vs RAY, Humongous Mecha smashing each other to death. It should be a Curb-Stomp Battle, since RAY was designed specifically to exploit weaknesses in the REX design... but REX is piloted by the Player Character, so it wins. Annoyingly, this doesn't stop Ocelot, who simply dashes down a pier and jumps onto his flagship: Outer Haven, the Arsenal Gear built under the Big Shell, still hosting GW and now featuring REX's railgun. Ocelot orders the ship to ram Shadow Moses, intending to simply squish Snake to death. However, in for his Taking the Bullet moment is Raiden. He—somehow—pushes Outer Haven back, slowing its rush long enough for Snake to scramble away. As his body sinks into the frigid waters, we are treated to flashbacks of the day he first met Rosemary.
Outer Haven retreats under fire from the newly-arrived USS Missouri; the latter is a WWII-era Iowa-class battleship, now used for training and not outfitted with SOP, modern naval weaponry, or tracking/radar systems, under the command of Captain Mei Ling. Snake and Otacon retreat to it whilst Raiden's body is fished from the water.
Chapter 5 - Old SunThe situation is grim. Outer Haven will be in position to fire on JD before long. The only hope for the world is for a small strike team to infiltrate Outer Haven and upload a virus, programmed by Naomi, into GW. In addition to sneaking through a giant submarine crawling with enemy soldiers, the person attempting to reach GW will need to make it through a hallway that literally microwaves everything inside it. Meryl, Akiba and Snake, the only able-bodied soldiers left, volunteer. Their plan calls for insertion of the strike team onto Outer Haven via catapults while the latter ship is above water to conduct the nuclear strike against JD, which, owing to Earth's gravitational field, unstable seas, and the accuracy and blast radius limitations of REX's railgun, can only be done when the satellite reaches its perigee 494 nautical miles (915 km) from the Bering Strait. The remaining sailors and Marines of the Missouri are meanwhile tasked with fending off the inevitable counterattack from Liquid Ocelot's forces, including automated Metal Gear RAYs. Drebin is also present to provide last-minute assistance by selling discounted "naked" weaponry and equipment to both the strike team and the Missouri crew. It's do or die time for our heroes, with the fate of the world at stake.
The infiltration begins poorly, with Meryl landing in the wrong part of the ship and Akiba missing entirely, plunging into the ocean. Snake continues alone, eventually reaching a central computer room. Here, Screaming Mantis, the leader and only surviving member of the BBs, makes her play, once again turning Meryl's weapons against her. Even worse, switching the controller port (or rather, switching which player the controller is assigned to) doesn't work. Snake has to shoot one of her mind-control dolls (shaped like Psycho Mantis and The Sorrow) out of her hands and use it against her. Afterwards, the spirit of Psycho Mantis appears and declares that he has been controlling Screaming Mantis, and through her the entire BB Corps, the entire time. He prepares to attack, but is banished by, of all people, The Sorrow, allowing Snake to progress.
Meryl offers to make a Last Stand holding the computer room. Snake continues onward but is ultimately trapped just outside the microwave corridor. Things look grim—the Mark III prepares to enter open combat, something it is clearly not equipped to do—until Raiden appears. Though he is armless, he can still hold his sword in his teeth... and electrocute people on command. He offers to travel to the server room, but Snake insists on doing it himself, in atonement for how The Patriots, Big Boss, and the Les Enfants Terribles clones have ultimately ruined the world as well as Raiden's life. So Raiden makes a Last Stand with only his sword, his teeth and his legs to defend him. Meanwhile, Meryl is on the verge of being overwhelmed until Akiba shows up. He explains that he is, and always has been, free of the control of Mantises and Ocelots everywhere because he has no nanomachines, making him a muggle in a World of Badass. It's also why he's never coordinated with Rat Patrol 01, who receive information from each other through the nanos. But when it's just him and Meryl, it's Battle Couple time. He reveals that he has loved her ever since that moment they first laid eyes on each other at Shadow Moses, and begs her to marry him. She refuses... preferring that she ask him instead.
Snake enters the microwave hallway. It's a Button Mashing minigame where Snake has to walk—crawl—drag himself—down the hallway, as his equipment overheats, as rounds from his weapons cook off, as the water in his body begins to boil and evaporate, as the artificial fibers of his muscle suit begin to glow white hot. In Split Screen, the travails of the battle—Johnny and Meryl becoming overwhelmed and running out of ammunition; Raiden being repeatedly subdued and knocked down by machete-wielding FROGs; the defenders on the USS Missouri under heavy fire and gradually taking casualties from Outer Haven's FROG detachment, weapons systems, dwarf gekko, and RAY units; Otacon dodging enemies and trying to hang onto his laptop (with which he is controlling the Mk. III) while Mei Ling prepares to defend herself with a pistol; Campbell and Rosemary pacing their office in helpless frustration—are displayed, underscored by a One-Woman Wail soundtrack that leaves most players hammering away at their controllers in agony. Once Snake gets through, the Mark III (apparently made of microwave-proof materials and totally unscathed) does all the work, leaving players with the nagging question of why Snake had to Escort Mission it at all. It's also one of the most powerful emotional beats of the franchise, and possibly in all of Video Games history.
The virus does far more than intended: it not only destroys GW, but also deletes JD and the remaining Patriot AIs as well. A video from Naomi then plays, explaining that Sunny helped her write the virus—or rather, that she helped Sunny. Using her knowledge of FOXDIE, Sunny crafted a virus which Naomi has dubbed FOXALIVE. It will wipe out the controlling elements of SOP and the entire Patriot AI network while leaving behind the code which helps keep the infrastructure of the world running. Outside, Ocelot's soldiers begin to collapse in emotional breakdown as their feelings and regrets, previously suppressed by SOP, come screaming back to them. The AI-controlled war machines, like the RAYs and three-armed dwarf Gekko, are all disabled en masse, with some even tumbling into the ocean. Mei Ling calls for a surrender. The world is saved, and our heroes have seemingly prevailed.
But Ocelot is not done. He drags Snake to the sail of Outer Haven for one last fistfight. It's the final battle of the franchise (or, at least, was thought to be, until Phantom Pain came out), and each of the fight's four phases uses the play controls, GUI, mechanics and audiovisual cues of each numbered game in the series released to that point. Finally, Snake wins, and Liquid Ocelot, who has now reverted to his original persona in his death throes as Revolver Ocelot AKA ADAM (70 years old), is defeated once and for all and ultimately dies. Before he passes, he manages to tell Snake that "I am Liquid's doppleganger, and you are his. Just like your father. You're pretty good.", even managing to perform his trademark hand gestures as a final "salute" of sorts for Snake. It's clear that in his final moments, Ocelot sees Snake as being equal to or better than Big Boss. Otacon then arrives via helicopter and airlifts a convalescing (and asleep) Snake to safety, privately wondering what the world lost and what it gained now that the Patriots were finally destroyed, heralding the start of a new and hopefully brighter future.
Epilogue - Naked SinAs Meryl dresses for her wedding, she and Campbell finally reconcile, and she asks him to walk her down the aisle. The other half of Rat Patrol 01 have recovered from their ordeals on the Volta: Jonathan stands for Johnny, while Ed officiates. Otacon and Sunny attend, as does Drebin, who reveals a number of secrets. First off, the Drebins are all Patriot agents, and he was ordered to help Snake eliminate Liquid, whom the Patriots viewed as their worst threat; likewise, Rat Pt. 01 were PatR10t agents. Meanwhile, Raiden recuperates in a hospital, having been restored to a very human-looking cyborg body. He is visited by Rosemary and her son by Campbell. Jack refuses to speak to them at first, but Rosemary has a confession to make: the whole thing was faked. She never had a miscarriage; the son she conceived with Jack just before the Big Shell Incident stands before them. And while she did marry Campbell, it was an elaborate hoax so that he could protect her and their son from the Patriots using them as leverage against Raiden. Overwhelmed, Raiden reunites with his family. Finally, Sunny begins to make friends her own age. She asks where Snake is, and Otacon, struggling against emotion, says only that Snake is ill and needs time to rest.
Solid Snake is in Arlington, standing before his father's grave. He has one last mission to carry out: to commit suicide to prevent a worldwide FOXDIE outbreak. He puts aside his last cigarette and brings his weapon (the Springfield Operator that he originally procured in Act 1) to bear. A shot rings out.
The credits roll. The expected list of voice actors appears, including someone named Richard Doyle playing... ...Big Boss???
Debriefing - Naked SonSnake couldn't go through with his plan and actually diverted his shot at the last second. He pants before the grave, overcome with exhaustion, frustration, and sweat. To his surprise, Big Boss suddenly appears and effortlessly dismantles Snake's gun, only to hug him and tell him to put the weapon down, as he didn't come to fight. Rather, it's time for them to talk. In a massive Info Dump, Big Boss fills in all that happened between the end of Snake Eater and today.
Not long after Operation Snake Eater, the six living members of the mission with ties to the West — Naked Snake, Ocelot, EVA, Zero, SIGINT and Para-Medic — gathered. With the help of the Philosophers' Legacy, they decided to fulfill The Boss's last wish: to create a world where nations would not discard soldiers for political expediency. Zero's method for accomplishing this was to rule the world from behind the scenes; after all, there would be no wars if the whole world was unified. In pursuit of this goal, Zero began to inflate Big Boss's reputation. Big Boss began to chafe under this agenda, having more interest in his own dream of a world where soldiers were free to choose their own fates and causes. The Les Enfants Terribles project was the final straw, and Big Boss left the cabal for good. EVA went with him, but Ocelot, clearly adept at playing the Double Reverse Quadruple Agent, agreed to remain as their spy in the ranks. The three of them watched as Zero's "Patriots" exploded in size and scope over the years, gradually becoming the colossal monster of Solid Snake's time—all driven by a tragic misunderstanding of what The Boss wanted. Although Big Boss attempted to put a stop to these machinations at Outer Heaven and Zanzibar Land, Solid Snake defeated him both times and rendered him comatose in the latter incident. Zero, not wanting to lose an icon and still bitter over the betrayal from someone he deemed a friend, then injected Big Boss's body with nanomachines to prevent him from ever waking up and to act as the biometric key to their system.
Both EVA and Ocelot were infuriated by this turn of events, and thus they hatched a long-term plan to rescue Big Boss and destroy the Patriots. Once it was time to act after the Shadow Moses incident, Ocelot, in order to fool the AIs, hypnotized himself into believing that the (recently-deceased) Liquid Snake could and would take over his personality via his arm. In particular, his actions, from as far back as the Shadow Moses incident to his role in maintaining and expanding the war economy to his ultimate death, were all meant to serve as a massive smoke screen for Solid Snake and his efforts to take down the Patriots. In fact, he even masterminded both of Naomi's "defections" throughout this incident specifically to get the FOXALIVE code to Sunny and Otacon in a way that wouldn't rouse the suspicious of the Patriot AIs. Big Boss's body, meanwhile, was gradually repaired using transplants from the corpses of both Liquid and Solidus. When FOXALIVE woke him up, he was able to locate Zero. The other two founding members of the Patriots are already dead; Para-Medic, known in civilian life as Dr. Clark, was the scientist who revived Gray Fox as a cyborg ninja, and was killed when Naomi helped him escape; SIGINT, real name Donald Anderson, became the head of DARPA and died at Shadow Moses under Ocelot's torture (supposedly an "accident"; by now, who knows). Big Boss has thus taken it upon himself to end the story by sending Zero "back to nothing." He has brought with him a wheelchair-bound (and comatose) Major Zero, plugged into catheters and breathing machines and all but a human vegetable at this point, and in front of Snake he disconnects the 105 year-old major's air supply. Not with a bang but a whimper, the mastermind of the Patriots ends.
Finally, Big Boss reveals that Snake carries a modified FOXDIE virus, injected into him by Drebin (by order of the Patriots) back in the first chapter. It is the real reason that EVA and Ocelot died, and it will shortly kill Big Boss as well. More importantly, though, it also displaced the starting-to-mutate original-FOXDIE that Snake still carried. Snake no longer needs to worry about becoming a walking plague carrier. Big Boss's only wish is for his son to spend what remains of his life in peace, telling him that "it's time to see the outside world with your own eyes."
Snake helps Big Boss over to The Boss's grave, and John salutes his mentor one last time. As father and son share a final cigar, Big Boss admits that he too misinterpreted The Boss's will: she wanted not to change the world, but rather "to leave the world the way it is." Big Boss passes away at the grave of a patriot who saved the world... and whose legacy changed it forever. His last words are, "This is good, isn't it?" Finally, and for all time, the Patriots are gone.
After the second set of credits, the last conversation of the game plays from Otacon to Snake. Snake declares that he will not only quit smoking, but also that he wants to "see this age off, see what the future brings" before his inevitable death in a year at most. Otacon (and by extension Sunny) in turn declares his intention to stand by him until the end and eventually pass on his story, and also that he still needs a partner to suffer through Sunny's eggs with in the meantime. After some hesitation, Snake agrees.
The game ultimately ends with a shot of Sunny successfully cooking a batch of sunny-side up eggs (having learned how to do so correctly from Naomi while she was the group during Acts 2 and 3), declaring that they're "sorta like the sun. It's rising again."
Four years after the events of the San Hieronymo incident, Big Bosswho prefers his original title, Snakeand Kaz Miller have established Militaires Sans Frontières, a small mercenary faction, on the Colombian coast. They are approached by Ramon Galvez Mena, a professor at the University of Peace, and his student, Paz Ortega Andrade. Galvez attempts to hire MSF to investigate an army that has discreetly occupied parts of Costa Rica. Snake refuses, identifying Galvez as a KGB agent, but is convinced when Paz plays a recording of The Boss.
When Snake arrives in Costa Rica, he begins to suspect that the mystery army has brought nuclear weapons with them. Enlisting the help of the Sandinista Liberation Army, he tracks a shipment to a research facility deep in the mountains. His suspicions are confirmed when he witnesses Hot Coldman, a senior CIA agent, announce his intentions to fire a live nuclear weapon as part of a project code-named "Peace Walker," a fail-deadly nuclear tank. Snake reveals himself to Huey Emmerich, one of Peace Walker's designers, who agrees to help him stop Coldman.
Following Huey's instructions, Snake ventures deeper into Costa Rica, searching for Dr. Strangelove, the designer of Peace Walker's artificial intelligence systems. He discovers that Strangelove has based Peace Walker's primary control systems on The Boss' personality. She demands to know whether The Boss genuinely defected to the Soviet Union, or if she died on a mission that was covered up, going so far as to torture Snake for information.
Snake escapes custody and attempts in vain to destroy Peace Walker, a quadrupedal nuclear launch platform. He chases Peace Walker across the Nicaraguan border to an American airbase on the shores of Lake Cocibolca. Discovering that the base has been occupied by Soviet soldiers, Snake infiltrates the facility to confront Coldman. Coldman reveals the purpose of Peace Walker: he believes that nuclear deterrence is a flawed theory, relying on humans to retaliate in the event of a nuclear exchange, whom he believes to be unwilling to destroy their own race. As an impartial artificial intelligence, Peace Walker would guarantee retaliation, and Coldman intends to fire a warhead to prove it. Suddenly, the facility is overrun by Soviet soldiers, led by Galvez, who reveals himself as Vladimir Zadornov. Zadornov intends to hijack Peace Walker for the Soviet Union, but the standoff is broken by the arrival of MSF and the Sandinistas, giving Snake enough time to destroy Peace Walker.
In the aftermath of the battle, Zadornov is captured and Coldman mortally wounded. In his dying moments, Coldman activates Peace Walker's data uplink, convincing NORAD that the United States is about to be hit by a Soviet nuclear strike. Snake contacts NORAD, and tries to convince them to stand down, but senior members of the armed forces refuse and plan to retaliate. With a nuclear strike imminent, The Boss' personality takes control of Peace Walker's damaged artificial intelligence and drowns Peace Walker in Lake Cocibolca, severing the connection and ending the threat.
Some time later, Zadornov repeatedly escapes from MSF, arousing Snake's suspicions that someone has betrayed them. Paz reveals herself to be the traitor, using Zadornov's escapes to seize control of Metal Gear ZEKE, a walking tank designed by Huey to act as MSF's deterrent against foreign intervention. Acting as an agent of Major Zeronow using the name "Cipher"Paz issues Snake an ultimatum: surrender MSF to Cipher and become his deterrent, or else she will fire a nuclear warhead on America, at which point they will be branded a nuclear-equipped extremist cult, and the world will unite in their pursuit of MSF. Snake prevents the launch by crippling ZEKE, and Paz is thrown into the ocean. In the aftermath, Snake reconciles with his memory of The Boss and accepts the title of Big Boss as he rallies the soldiers of MSF to prepare for a fight for their survival, declaring them to be living in "Outer Heaven".
Though the War Economy has collapsed, PMCs are still in big demand. Most have moved towards employing cyborgs as ground forces, since they have superior strength, speed, stamina, reflexes and durability. Raiden works for one of them, called Maverick. As the game opens, we find him and his cohort providing bodyguard detail for President N'mani, who has brought peace to Africa. Raiden approves, as he follows the way of the samurai (despite being, technically, a cyborg ninja) and views his sword as "a tool for justice." Unfortunately, the peace train is derailed by other cyborg attackers: a fellow named Sundowner, who wields two machetes as scissors, and Jetstream Sam, who practices iaido and fires his sword out of a sheath fashioned from an M-16 assault rifle. Sundowner murders N'mani and Sam makes short work of Raiden.
Three weeks later, Raiden is in a new cyborg body. Under orders from Maverick's leader, Boris, Raiden is sent to a beakaway nation called "Abkhazia." Maverick's support team — tech expert Kevin, data analyst Courtney and cyberneticist Doktor — have identified Jetstream Sam and Sundowner as members of "Desperado," a PMC involved in terrorism, who are currently leading a coup in the nation. Desperado assign a prototype AI in a canine body, "Bladewolf," to defeat him, but Raiden is able to overpower him. He then faces Mistral, a member (alongside Sundowner and Sam) of the "Winds of Destruction," the Quirky Miniboss Squad that run Desperado. Raiden picks up the signature weapon of each miniboss he defeats, which is then available as an alternate weapon; in Mistral's case, this gives him a polearm made of the arms of Dwarf Gekko.
Raiden and Bladewolf are assigned to investigate a facility in Guadalajara, Mexico, where some sort of human trafficking is taking place. After meeting an escaped victim, a pre-adolescent named George, Raiden learns that the facility is pulling the brains out of kids and shipping them to America for training as future-cyborg Child Soldiers, either by Desperado or by World Marshal, a PMC associated with US Senator Steven Armstrong. Since child soldiers are Raiden's Berserk Button, he pledges to free the children. He is largely successful, though a doctor manages to take George captive, forcing Raiden to slice through the child (with George's consent) to get to the doctor.
With George safely upgraded to a cyborg, Raiden resigns from Maverick to wage a one-man war against World Marshal headquarters in Denver, CO and rescue the child-soldier-brains. Boris is obliged to officially condemn his actions, but Maverick continue to provide off-the-record support throughout, having decided where they want to come down when they have to choose To Be Lawful or Good. Raiden first battles the sai-wielding Monsoon, the final member of the Winds of Dstruction to be introduced; his body uses an electromagnetic variant of Detachment Combat to separate into tiny segments, making him practically intangible. At the top of the building he also faces Sundowner, whose body includes damage-proof shields on articulated arms in addition to his machete-scissors. During this assault, Raiden becomes increasingly distraught by his own actions and sinks back into his childhood persona, Jack the Ripper, before finally embracing it as his Limit Break. He is ultimately successful in his mission, allowing Doktor to escape with the brains. However, he learns from Sundowner that Armstrong brought World Marshal and Desperado together to affect an assassination on American President Hamilton, who is heading to Pakistan for peace talks. Even worse, the plan is set to go off in only a few hours, and Raiden is on the wrong side of the planet to stop it.
To get to Pakistan, Raiden gets in contact with a company called Solis, run by none other than the child prodigy Sunny Gurlukovich. She has developed a spaceplane which will get Raiden to Pakistan with several minutes to spare. However, the way is blocked by Jetstream Sam, who has a final showdown with Raiden. Bladewolf, who served Sam prior to being turned by Raiden, is remorseful over the outcome, and takes Sam's HF blade to remember him by; Sam's is the only Miniboss weapon that Raiden doesn't get to wield as an alternate weapon.
Shabhazabad Air Base is quiet... too quiet. Raiden, infiltrating the base, finds Wolf's damaged body laid out for him, clearly as bait. Bait for what? Metal Gear EXCELSUS, a spider-tank piloted by none other than Senator Steven Armstrong. Armstrong reveals that Raiden has played directly into Armstrong's hands, since — even though Raiden does wreak enough havoc at the airbase to convince Air Force One to turn around — his actions will be misconstrued as the assassination attempt, and the American people are crying out for revengeance. Armstrong, with his connections to PMCs, will win any presidential election in a landslide. This would give him free rein to realize his vision of a society where only the strong survive, fighting and dying only for what they believe in — not for a company, nation, war economy, or anything else.
Though Raiden defeats EXCELSUS, he discovers that Armstrong is no pushover: he has augmented himself with "Nanomachines, son!" that make him Nigh Invulnerable. Armstrong snaps Raiden's sword, but Bladewolf throws him Sam's, which kicks in a Heroic Second Wind. Raiden fully embraces his Jack The Ripper persona, declaring that he has changed his mind about his sword being a tool of justice. "Besides, this isn't my sword."
In the aftermath, Maverick receives government approval to begin outfitting the rescued brains with cyborg bodies, with the intent of establishing (for all intents and purposes) a cyborg temp agency. Bladewolf and George have gone to Solis to work with Sunny, with the latter two showing some romantic sparks. However, PMCs remain ubiquitous, especially with US-Pakistani tensions set ablaze by the incident at the airbase. And Raiden has been changed; as Armstrong himself accused him during their fight, they are Not So Different, and Armstrong's memes of being The Unfettered will live on in Raiden whether Jack likes it or not. Consequently, Raiden resolves against returning to his wife and son in New Zealand, nor against rejoining Maverick: "I have my own war to fight."
In the aftermath of the Peace Walker incident, Paz Ortega Andrade is missing and presumed to be dead. Under the direction of Kazuhira Miller and Huey, Militaires Sans Frontières turn their attention to an upcoming inspection by the UN amid suspicions that they possess a nuclear weapon, which MSF believes to be an attempt by the Cipher organization to stifle and retaliate them. Their preparations are interrupted when MSF agents in Cuba investigate reports that Paz survived and has been detained at Camp Omega. Futhermore, Ricardo "Chico" Valenciano Libre attempts to rescue her and is similarly captured. Believing that both of them could compromise MSF, Snake is sent to infiltrate Camp Omega and extract them if they are alive, or confirm that they are dead and if so, determine what they revealed to their captors. Snake also recognizes the value in rescuing Paz, as he believes doing so will convince Cipher to stand down while Paz will be more willing to discuss Cipher's activities with MSF.
Snake infiltrates Camp Omega as a mysterious Special Forces unit known as XOF simultaneously departs via helicopters. He locates and extracts Chico, who claims Paz is dead. Using a recording that Chico gives him, Snake and Miller deduce that Paz is alive, and was moved deeper into the camp. By collecting audio cassette tapes around the base, Snake learns that Paz and Chico were tortured, physically and psychologically, for information about the MSF base. Chico, after being tortured and forced to sexually assault Paz, tells Skull Face the location of the base and what defenses there are. In a later recording, Paz is heard calling Chico a "coward" and "traitor" for giving up the information; however in the final tape she records herself saying she forgives Chico and would not have made it through the torturous interrogations without him.
Snake ultimately manages to rescue Paz as well, with the group escaping via an MSF helicopter designated Morpho One. However, on the way back to Mother Base, Chico discovers that Paz was surgically implanted with a bomb, prompting Snake and an MSF medic to remove it by hand. They then arrive to Mother Base to see it in flames as XOF forces attack. Morpho One lands long enough for Snake to rescue Miller, who claims that the UN inspection was nothing but a ruse for the XOF ambush, which razes Mother Base. As they attempt to escape XOF, Paz regains consciousness and warns everybody that there is a second bomb inside her body. Knowing that she is about to die, she jumps out, trying to throw herself clear of the helicopter. She succeeds, but the explosion causes Morpho to spiral out of control and collide with a pursuing XOF helicopter. Snake is knocked unconscious.
The epilogue reveals that the United States government downplayed MSF's destruction and attempted to cover up their dealings with the organization, as do many of MSF's clients. There are no known survivors of the assault, apart from Snake, Miller, and Huey.
In a post-credits scene, set prior to Snake's arrival at Camp Omega, Paz is being interrogated by Skull Face, who demands the whereabouts of Cipher / Zero, as Paz had met Zero in person. Paz eventually gives in and agrees to tell him Zero's location before the scene ends.
Chapter 1 - RevengeIn 1984, Big Boss awakens in a Cyprus hospital after a nine-year coma. Immediately the word goes out that "V has come to." Big Boss is alarmed to note that he has lost his left arm in the helicopter crash, and even more alarmed when, barely seven days after his awakening, a Cipher assassin is sent to kill him. Only the intervention of the patient in the next bed, calling himself "Ishmael," allows them to survive. Ishmael tells Boss that "You're talking to yourself", and helps him escape. It's a Tutorial Level from hell: Cipher's black-ops strike force, XOF, are attacking the hospital and putting bullets into every body they find, whether it's breathing or not. Even worse, there's a Man On Fire—no, like, literally, someone who is on fire and absorbs bullets before spitting them back out at whoever shot them—plaguing the place, killing just as indiscriminately as the XOF strike force is. (The Man On Fire has a kid in a gas mask trailing him at all times, levitating.) Eventually Boss and Ishmael make their escape, but their ambulance is derailed by a flaming whale (no, really), and when Boss wakes up, Ishmael is gone. But help is on the way: Revolver Ocelot arrives to extract him on horseback; the two travel to a new Mother Base in the Seychelles.
Big Boss, now calling himself Venom Snake or Punished Snake, learns that, in the intervening nine years, Kazuhira Miller has established a new mercenary unit, the "Diamond Dogs," to replace MSF. Unfortunately, Kaz himself has been kidnapped by Russian forces persecuting the invasion of Afghanistan; though Snake is able to exfiltrate him, he has already lost An Arm and a Leg. Snake also encounters the Skulls for the first time, soldiers who have a Flash Step teleport and blanket the area with mist. Kaz, remaining in control of the Diamond Dogs, sets the group's agenda: to find Skull Face and get revenge for everything he has cost them.
One new wrinkle in the game is the Buddy system. Snake allowed to pick one of four companions who will deploy with him onto the battlefield and give him aid. The original is, literally, the horse he rode in on: D-Horse, whom Snake can use to traverse terrain quickly. D-Dog (probably actually a wolf) sniffs out enemies, as well as helpful collectables. D-Walker, a man-sized mecha, comes equipped with chainguns, rockets and other heavy ordnance, and is not meant for stealth. Finally, Snake encounters the last of his buddies whilst on a mission: Quiet, the assassin Cipher sent to kill him in the hospital. She no longer speaks, but has traded her voice for other abilities, such a teleport similar to that of the Skulls. She also wears almost nothing, the justification being that she photosynthesizes and breathes through her skin and would suffocate if she didn't have her boobs hanging out. After Snake defeats her in a Sniper Duel, he may choose between executing her and returing her to Mother Base. If he spares her, she will eventually volunteer to serve at his side. She can be used to infiltrate outposts, and provides cover fire for Snake with her sniper rifle.
After some operations in Afghanistan, Mother Base receives a transmission from Huey, who has announced his intention to defect. Snake finds him in a power plant, where he's hard at work on a Metal Gear prototype called Sahelanthropus. As Snake watches, Emmerich is forcibly ejected from the project by Skull Face and taken to the Soviet Base Camp in Afghanistan. Snake must infiltrate this base, the hardest mission in the game to date owing to its enormous size, but Huey at least has a new toy for Snake to play with: a Walker Gear, of which D-Walker is an example. During the exfiltration, Sahelanthropus comes to life and starts chasing after Snake and Huey—despite Emmerich's protestations that no such thing should be possible, as the mecha's controls are unfinished. Fortunately, Pequod, the extraction helicopter, comes with enough dakka to put the machine down.
Though Ocelot and Miller (and, for that matter, Snake) are convinced that Huey was complicit in the UN inspection which brought MSF down around their ears, Huey protests his innocence. He does provide some useful intelligence: that Zero has been increasingly absent from Cipher's activities, and that Skull Face has more or less taken over the organization. He also reveals that Cipher are focusing a lot of funds on activities in Africa, where supposedly they are building "a weapon to surpass Metal Gear". As a result, Snake finds himself dropping into the Angolan Civil War. On several missions, he finds corpses tossed on fires for disposal, and in one case a large group of bodies hidden in a lake with strange purple growths on their chests. Snake also discovers a group of Child Soldiers being deployed in battle. He rescues them, and Miller makes space for them on Mother Base where they will receive an education and learn more than soldiering.
One of those children reveals that their former leader had been taken away to an industrial zone called "The Devil's House." He requests that Snake rescue the boy. Infiltrating the industrial zone, Snake enters a warehouse whose floor is coated with blood, scraps of flesh, and viscera. Within are soldiers, boys and men both, strapped to beds. Slits down their throat contain earbuds, which recite dialogue in specific languages. There is no apparent correlation between the language and the soldier being fed it. Many of the soldiers feature the strange purple growths Snake discovered on the bodies in the lake. And Skull Face is clearly behind it all, as Snake spies him executing one of the prisoners. When he (Skull Face) sees Snake, he simply summons the floating boy and the Man on Fire to handle him, burning the whole place down. Snake returns to Diamond Dogs with more questions than answers.
Snake receives news of a group of child soldiers taking over a village and conducting savage raids on the local populace. He is tasked with removing their leader, a boy named Eli. Eli is blonde and pale-skinned, somewhat incongruously for this area of Africa, and puts up an impressive fight. Even after being integrated into Mother Base, Eli shows an enormous amount of arrogance, often attacking grown soldiers—and coming decently close to defeating them. Miller becomes suspicious that Eli is one of the products of the Les Enfants Terrible project and has some DNA tests done. However, the tests come back negative: Eli is not related to Venom Snake.
After Snake is assigned to rescue two American technicians who were sent to observe the Devil's House by Skull Face, Quiet breaks dormancy, attempting to kill a member of the Diamond Dogs. Shortly thereafter, a strange epidemic sweeps through the ranks, killing many, including the soldier Quiet attacked. Ocelot and Miller create a quarantine platform where symptomatic soldiers may be kept, but have no idea what the common link between all of them are. It's Snake who notices (or looks up on the Internet) that all of them speak Kikongo. By quarantining everyone who knows that language, the Diamond Dogs are able to contain the spread of the disease, but they have no idea what it is, much less how to cure it.
A desperate quest for information brings Snake to a manor house, where an ancient Navajo man named Code Talker resides. He reveals that he has been doing research into vocal cord parasites. These ancient creatures once gave man the ability to talk, but have now been cultivated to consume the lungs of anyone who produces particular sounds. Skull Face is training them to activate in response to sounds specific to each language, thus allowing him to wipe out anyone who speaks it. Skull Face has also developed modified versions of the parasites that replace the infectee's skin; the Skulls get their powers from these parasites, as does Quiet. Even more than that, Skull Face has been setting himself up as a broker of nuclear weapons, but also installing fail-safes in each warhead so that it will not detonate without his approval. With Code Talker on staff, Diamond Dogs are able to clean up the parasite infestation. Ocelot and Miller also use their newfound understanding of Skull Face's plans to convince Huey into confessing the location that Sahelanthropus is being stored: OKB Zero, a secret Russian base in Afghanistan.
After infiltrating the base, Snake confronts Skull Face. Unfortunately, he's outnumbered by XOF soldiers (who will have respawned even if Snake cleared out the entire base on his way in — which many players likely did; the base is so cramped and well-lit that a stealth approach is almost impossible), and Snake surrenders. Skull Face drives him back to the power plant while giving his Villain Monologue: as a child, he was stripped of his native language and culture, and forced into various roles—including as John's back-up for Operation Snake Eater. He plans to release the English-speaking parasites as revenge on Zero, and then set himself up as the only nuclear power in the world.
At the Power Plant, Skull Face attempts to set the Man on Fire against Snake. But the floating child refuses to acknowledge his orders. Acting on the wishes of another, the child activates Sahelanthropus, which rampages through the XOF strike force and comes for Snake. Snake destroys it, and then jumps on a chopper with Miller to go visit Skull Face, who was wounded in the chaos. They open his container of English-speaking parasites and discover one of them missing; Snake throws the other two in the fire, and fails to notice that the floating child intercepts one of them. He and Kaz get their revenge on Skull Face by blowing off An Arm and a Leg. They intend to leave him to die in agony afterwards, but Huey, missing the point of their revenge, puts him out of his misery.
Back on Mother Base, the Diamond Dogs celebrate their triumph. Huey is over the moon—not only to have accomplished his own revenge against Skull Face, but to have Sahelanthropus back in his possession. As the credits roll, though, Snake and Miller acknowledge that, revenge or no, they will always suffer their phantom pain. Additionally, out of sight, the floating child provides his pilfered vial of English-speaking parasites to Eli.
Chapter 2 - RaceThough Skull Face is dead, the Diamond Dogs continue to perform clean-up, tracking down any data on the vocal cord parasites, not to mention anyone seeking that data, and confiscating it all back to Mother Base. Though there are some new missions in this chapter of the game, others are simply missions from Chapter 1 with added limitations on them. Some players were critical of this choice.
The Diamond Dogs retrieve an AI Pod which Huey had been working on at the Soviet base camp. Inside the pod is the corpse of Strangelove. Huey is unable to provide a believable alibi as to her death, but he does acknowledge that he and Strangelove had a son together—a child named Hal, who will one day call himself Otacon. Huey claims not to have seen his son for years.
Events also continue to brew around Quiet. It all starts when one of the rescued kids drops Shabani's necklace into a tank of chlorine disinfectant. Quiet takes some injuries to retrieve it, and it becomes clear that Venom Snake has become very attached to her. Miller attempts to interrogate her, revealing what they've found: her burnt lungs contain traces of flower petals found near the hospital in Cyprus, and she has clearly been infected with Skull Face's modified parasites. Ocelot stops the interrogation, pointing out that she's had plenty of chances to cause mayhem—technically, she still lives in the brig, under guard—and clearly has not done so. (True, she tried to kill that soldier one time, but when one considers that he might have been the source of the Kikongo-speaking parasites, this was an understandable and arguably justifiable act.) He recognizes that Quiet serves Snake because she loves him, a motivation both Miller and Ocelot have some personal experience with. Snake concurs, and has her released. It's Code Talker, speaking to Quiet in Navajo, who gets the truth out of her: she was ordered by Skull Face to spread the English-speaking parasites to Mother Base, through the simple expedient of having been infected with them herself. To this end, Quiet has vowed never to speak English again, thus saving both herself and the entirety of Diamond Dogs.
The secrets concerning the floating child, Tretij Rebenok, and The Man On Fire are gradually unraveled. The Man on Fire is in fact the corpse of Volgin, thirsting for revenge, but relying on the floating child for his powers. Tretij, who will one day be called Psycho Mantis, is revealed to not have full control over his powers; instead he is drawn to whoever's Roaring Rampage of Revenge is strongest and carries out their wishes. In controlling Sahelanthropus, he was actually responding to Eli. Eli eventually organizes a mass break-out from Mother Base, taking Psycho Mantis, his child followers and Sahelanthropus with him back to Africa. Since Sahelanthropus has a child-sized cockpit, Snake asks Huey if he ever asked his son to try driving the thing. Huey's evasive answer suggests that he was lying when he said he has not seen Otacon in several years. As to Eli himself, his fate is Left Hanging due to Kojima Productions having to rush out the game, though records of incomplete levels have been discovered that give closure to this arc. The events of this cut mission are still canon per Word of God, and, as such, they have been included in this recap (though at the end, as exactly when they take place chronologically is slightly hazy).
English-speaking parasites erupt on Mother Base. They have mutated to the point that Code Talker's treatments are ineffective, forcing Venom Snake to execute many of his own people. The breakout is traced back to Huey's lab, where he was experimenting on them. Huey is put on trial, and during this time the truth about Strangelove's death is revealed: Huey killed her after, yes, he did try to force the 2-year-old Otacon to drive Sahelanthropus and his mother protested. Additionally, evidence is presented that Huey colluded in the "inspection" that destroyed MSF nine years ago. Venom decides against executing Huey for his crimes, but instead inflicts punishment of Cruel Mercy upon him. Huey is exiled from Mother Base, left adrift in a life raft and robbed of his mechanic legs, still protesting his innocence.
Quiet leaves base without permission and is captured in Afghanistan. Since she herself is living evidence of how to work with parasites, Snake needs to get her back. The Battle Couple fight off an army together, but as they attempt to retreat, Snake is bitten by a cobra. Quiet attempts to vector in the evac chopper in Navajo, but is ultimately forced to speak English. By the time Snake regains consciousness, she's walked away into the desert and is removed from the player's available companions forever. (Konami eventually patched in a way to bring her Back from the Dead after fan outcry, though the player is required to jump through a number of hoops to do it.)
Finally, Venom Snake discovers that hypnotherapy was performed on him. He discovers this because he starts having flashbacks to Paz's death and the subsequent helicopter crash. In these flashbacks, he is not Big Boss — he is the medic. Though Big Boss did indeed enter a coma, he recovered quickly. Ocelot then came forward with a plan — proposed by, of all people, Zero — that The Medic be surgically altered to look like Big Boss, and brainwashed to believe so as well to act as an unwitting Body Double for Big Boss. The two Big Bosses simply hung out in Cyprus until XOF finally found them, at which point Big Boss — "Ishmael" — helped Venom Snake escape. While Venom was out cold, Ocelot extracted him from the crashed ambulance first and sent him on his way, and then doubled back for Venom Snake. This is why Eli (who is indeed Liquid Snake) did not match "Big Boss's" DNA. The real Big Boss has been building up Outer Heaven all this time, in preparation for their bid for freedom. The Medic eventually receives a tape recorded for him by the real Big Boss, who thanks him for his service.
- "Now do you remember? Who you are? What you were meant to do? I cheated death, thanks to you. And thanks to you, I've left my mark. You have too. You've written your own history. You're your own man. I'm Big Boss, and you are too. No... he's the two of us together. Where we are today, we built it. This story, this legend; it's ours. We can change the world, and with it, the future. I am you, and you are me. Carry that with you wherever you go. Thank you, my friend. From here on out... you're Big Boss."
The credits reveal that Venom Snake continued to serve as Big Boss's decoy until 1995, where he died in Outer Heaven at the hands of Solid Snake at the end of Metal Gear 1. (The real Big Boss presided over the operation, faked his death, and surreptitiously escaped to Zanzibarland.) So, clearly, he wasn't too upset at the issue. The person who is upset is Kaz; in the post-game phone call with Ocelot, he learns the truth behind Big Boss' plans. Outraged at Big Boss' deception and being subsequently kept out of the loop, he breaks with Big Boss and Outer Heaven entirely, promising to aid Venom Snake and whichever one of the Les Enfants Terribles sons that Cipher will send to eventually take down Big Boss. Ocelot, for his part, declares his intention to take the opposing role, helping the rebel son, setting the stage for the conflicts in Metal Gear Solid. He also speculates that eventually, one of them would have to kill the other should Kaz actually follow through with his threat. The latter agrees, but for the meantime declares that they both "get used to coexisting."
Cut Content — Mission 51The Diamond Dogs keep up their search for the escaped Eli, his gang of child soldiers, and Sahelanthropus. Miller briefs Venom, revealing that the intel team has managed to narrow down the search area to somewhere in central Africa, as they were able to recover the kidnapped helicopter pilot. He was left alive, most likely as a taunt from Eli's and his boys for Diamond Dogs to try and find them. Miller, however, also notices that there are rumors of men going around to villages in the area and asking for witnesses who saw "the giant in the sky". Both Venom and Miller realizes that it means that the remnants of XOF, now reintegrated with Cipher after the death of Skullface, is still actively trying to recover Sahelanthropus. Miller cautions that if they are successful they won't just be getting their hands on the Metal Gear: Eli is infected with the last surviving English-language parasites.
Sometime later, the intel team has a breakthrough, managing to pinpoint Eli and his gang's location to a small island in a salt lake in Central Africa. Here Eli has established "the Kingdom of the Files" that he has always dreamt about. The bad news are that he and his gang are all likely infected with the parasites by now, and have in all probability spread the infection around the island; the good news is that Eli and the boys are safe for the time being, as the parasite won't affect you if your voice hasn't yet broken; and the parasites are unable to cross salt water under their own power, and so remains contained to the island for the time being. So far, Eli has only communicated with the outside world on one occasion: by offering to return the nuke on Sahelanthropus in exchange for the corpse of Big Boss.
Venom approaches on the island with instructions to eliminate the English-language parasites, recover Sahelanthropus, and rescue the children, Eli included. Once he has safely completed his objectives and evacuated, Diamond Dogs plans to carpet bomb the island with napalm to make sure any remaining parasites are destroyed. Time is of the essence; an intercepted radio transmission reveals that Eli's voice, due to his accelerated aging, is starting to change, and his parasite infection will soon turn active.
Upon landing on the island, Venom finds that XOF troops has already begun a strike operation to kill Eli and take Sahelanthropus back. Many of them have been killed by cruel booby traps set by Eli's boys, but a good number of them have survived. Evading both the traps and the XOF forces, Venom makes his way to the center of the island, where he finds Eli resting in Sahelanthropus' cockpit among the child soldiers. However, it turns out a platoon of XOF soldiers has beaten him there, opening fire on Eli. Tretij Rebenok renders their weapons useless with his psychokinesis, but Eli is already angered; he activates Sahelanthropus and begins killing the soldiers, until he eventually discovers Snake hiding nearby from the attack. He stops his onslaught momentarily to speak directly with Snake and declares that he is going to get his revenge, and the two then begin a long and epic battle across the island, involving all departments of Diamond Dogs in the fight.
Venom and Eli's battle eventually comes to a close when Sahelanthropus' torso is blown in half at the waist, causing it to shut down and become inoperable. As Eli emerges from the cockpit, he is approached by a squadron of XOF soldiers ready to kill him. Venom is able to distract the assassins by springing a surprise attack on them, but he suffers a head injury while seeking cover from their counterattack. Unable to differentiate between red and white, he mistakes Eli's red pilot suit for XOF's white suits and accidentally shoots the boy. Venom runs to Eli's motionless body with a Big "NO!".
The Diamond Dogs arrives in force, along with Ocelot, to evacuate Eli's boys and assess the damage to Sahelanthropus. A field medic takes a look at Eli and discovers that he is wearing a Bulletproof Vest, and was only knocked unconscious by the shot. Venom orders that Eli to be taken back to Mother Base and be patched up, but Eli starts to come around, coughing violently. The field medic and Diamond Dogs jump back in horror: Eli's parasites are starting to break dormancy. Venom, however, leans closer as Eli laughs spitefully at him. Eli goes on to lament that he is a creation of Cipher, and his fate was written into his genes, but since he came out flawed, it makes him a loser. He blames Venom for all of what has happened to him (believing him to be the real Big Boss), and angrily declares that he aims to surpass him and destroy both him and Cipher. Ocelot pulls Venom aside, reminding him that they need to commence the bombing soon, and orders the Diamond Dogs to begin evacuating the island.
As his men leave, Venom takes out his gun and points it at Eli, preparing to Mercy Kill him. But he finds he cannot pull the trigger, telling Eli that he is "one hell of a soldier." Eli just snarls that he is going to kill him. In response, Venom unloads his gun, leaving just one bullet in the chamber and places it in front of Eli, telling him: "That's right. Don't blame yourself. Blame me." He then returns to the helicopter, letting Eli decide how to use the single round.
Eli, furious, momentarily aims at Venom's back, but reconsiders. He watches the Diamond Dogs leave the island with the broken remains of Sahelanthropus, and puts the gun to his own temple... only to discover that Rebenok has appeared next to him. Eli lowers the gun as Rebenok now appears in front of him and stares silently into his eyes. With a slow movement of his hand, Rebenok pulls the parasite infection from Eli's body and out through his mouth, before tossing them aside. Rebenok then turns around, and start hovering upwards, pausing to extend his hand towards Eli. Eli takes his hand, and the two them levitate away, just as the Diamond Dogs starts their bombing and the island is engulfed in an inferno. Back in the helicopter, Venom and Ocelot watches the bombing of the island from afar. Venom, however, looks at his own reflection in the helicopter's window and can only see a blood-soaked demon.
Elsewhere, Eli, a bit unsteady on his legs, is wandering the wilderness. He falls to his knees and takes a brief moment to gather himself. As he rises to his feet again, it is revealed that Rebenok is still with him, quietly following behind him. Eli stares determined ahead as he keeps on walking, declaring "Not yet. It's not over yet."