- After awakening from a nine year coma, Big Boss forms a new mercenary group called, Diamond Dogs, and teams up with his former rival, Ocelot, to track down the men responsible for the destruction of MSF.
- In the aftermath of the events of "Ground Zeroes" and the destruction of Militaires Sans Frontières, Big Boss falls into a coma. Nine years later, he awakes and forms a new mercenary group, the Diamond Dogs. Now under the guise of the codename "Venom Snake", he ventures into Afghanistan during the Soviet war to track down the men responsible for MSF's destruction. Along the way, he becomes reacquainted with his former rival Ocelot and encounters a unit of warriors robbed of their past, present and future. While he and Kazuhira "Kaz" Miller are initially driven to exact revenge, Snake soon unearths a plot by the Cipher organization to develop a weapon with the potential to surpass even the Metal Gear system, and his mission quickly switches focus to ending this new threat.—Steven Vo
- The year is 1984, where a solider known as many names but mostly known as Snake has awaken from a nine year coma. As he awakens he remembers the destruction of his mother base from a network known as Cipher. Filled with nothing but vengeance Snake has formed a a new unit "Diamond Dogs" so he can lead a path of vengeance for the phantoms of MSF. What started Ground Zeroes will end V.
- After the fall of Mother Base 9 years prior, tactical legend Snake falls into a coma. When he wakes up in a Cypriot hospital, he see'a that he has lost his left arm, and that there's shrapnel lodged in his skull, and debris still in his body, he escapes from the hospital with the help of a mysterious man when the people who are hunting him down, the Cipher network, attack. Now back onto the field, Snake, having adapted the persona of Venom Snake, reunites with former rival Ocelot and friend Benedict 'Kazuhira' Miller to rebuild Mother Base and avenge themselves by destroying Cipher. But that is no easy task. Even though Snake is alive, the whole world wants him dead.
- 21 years before the events of Shadow Moses in Metal Gear Solid (1998), Snake's father, Big Boss, was building the ultimate military base to end the exploitation of soldiers from governments across the globe: Outer Heaven. Big Boss' dream is facing one of many hurdles in its path: the genocidal psychopath, Skull-Face, wants to cleanse the Earth with parasites that can infect people through one's mother-tongue. With the fate of the world at the mercy of Metal Gear, Big Boss must stop it and Skull Face from unleashing untold disaster upon the planet.—Johnny
- Following the destruction of Militaires Sans Frontières (commonly abbreviated as MSF) at the seeming hands of the Cipher organization, Big Boss(Kiefer Sutherland) falls into a coma which lasts for 9 years. Soon after his awakening in 1984, the Cipher assassin Quiet(Stefanie Joosten) makes an attempt on his life. Big Boss is rescued by a mysterious man wearing bandages on his face who calls himself Ishmael. While further trying to escape the hospital the two become caught in the crossfire between Cipher soldiers aiding Quiet and the telekinetic Tretij Rebenok, "The Third Child", helped by his apparition, The Man on Fire(Dave Fouquette). After a relentless car chase, Ishmael disappears, leaving Snake to continue his escape with Revolver Ocelot(Troy Baker), now working with a new mercenary company called Diamond Dogs, founded by Kazuhira Miller(Robin Atkin Downes) as a replacement for MSF.
While searching for clues on Cipher and extending Diamond Dogs on an offshore platform near the Seychelles, Big Boss and his new, growing mercenary company become involved in the SovietAfghan War in Afghanistan and in the Angolan Civil War on the Angola-Zaire border. Along the way Big Boss recruits the Cipher agent Quiet, who meanwhile seems to have acquired supernatural abilities and no longer speaks; the scientist Dr. Huey Emmerich(Christopher Randolph), who's suspected of selling out the MSF in Ground Zeroes; a spiteful, British child, Eli(Pier Stubbs), speculated by the Diamond Dogs to be one of Big Boss's clones who is leading a band of runaway child soldiers; and finally Code Talker(Jay Tavare), a Navajo expert on parasites working for Cipher who has a strange enthusiasm for hamburgers. Meanwhile Big Boss begins to encounter the Skulls, deadly enemy soldiers who have similar abilities as Quiet. The Diamond Dogs also suffer an epidemic, losing many soldiers before it is stopped.
It is eventually revealed that the organization that lead the attack on MSF in 1975 was only previously a part of Cipher, having gone rogue since. Its leader, Skull Face(James Horan), sees Cipher's plan to make the world one as effectively making it culturally American. To avoid this, he intends to release a parasite, in part developed by Code Talker, that grotesquely kills anyone who speaks the English language. A modified version of this same parasite is used to give Quiet and the Skulls their unusual abilities while a strain targeting a different language than English was the cause of the earlier epidemic. After having released the parasite, Skull Face finally plans to make nuclear weapons available to as many minority groups as he can. By way of nuclear deterrence he imagines no one will dare compromise anyone else, protecting the cultural integrity of each group and attaining world peace. To ensure a nuclear war doesn't actually happen, he secretly plans to maintain remote control of all the weapons.
To make nuclear weapons desirable again, Skull Face first wants to let loose a new model of the Metal Gear system known as the ST-84 "Sahelanthropus", hoping to start a new cold war. As it is unfinished, he uses The Third Child's paranormal abilities to control it, but during the test the psychic turns against him, having Metal Gear crush the Burning Man and trapping Skull Face himself. Big Boss defeats the rampaging Metal Gear and has his revenge on Skull Face with Miller. Later it is explained that The Third Child was not consciously working for Skull Face. Rather, being psychic, because of his sensitivity to other people's thoughts, he would come to personify the most vengeful person around, wreaking havoc on their behalf. In the hospital he had been driven by the The Man on Fire's hate for Snake who thwarted his plans in the past. Under the Metal Gear demonstration, he had picked up on Eli's animosity towards his likely father, Big Boss.
In the aftermath of the Skull Face situation, Eli, along with The Third Child and the rest of the child soldiers, steal the remains of Metal Gear. Meanwhile, Huey Emmerich, trying to make money on the parasites, accidentally mutates them and causes a second epidemic, forcing Snake to personally kill many of his own men to contain it. Instead of pouring their ashes into the sea, he decides to make them into diamonds so that they can be diamond even in death. Additionally, Huey is accused of being involved in the attack on MSF, and evidence proves that he murdered his wife, Dr. Strangelove, due to an argument over using their son as a test pilot for Metal Gear. As a result, Big Boss exiles Huey from Diamond Dogs.
If the player meets certain requirements, in a hidden mission, it is revealed that Quiet was infected by the English strain of the parasites and sent to join Big Boss by Skull Face so she could spread it among them as a last resort, until her time with them made her genuinely change sides. After being forced to speak English to save a poisoned Big Boss, not wanting to risk causing an epidemic, she disappears. If the player meets certain other requirements it is also revealed, in another hidden mission, that the real Big Boss was in fact Ishmael at the beginning of the game, and that the Big Boss the player has been controlling all along was actually an MSF medic (who had assisted the real Big Boss during the MSF attack) given plastic surgery and hypnosis to become a second Big Boss, and used as a decoy for Big Boss's enemies.
Ending text states that this second Big Boss, "the Phantom" as referred to by Ocelot who knew of this, goes on to set the events of the Outer Heaven Uprising in motion, where he eventually dies at the hands of Solid Snake. The real Big Boss eventually resurfaces during the Zanzibar Land Disturbance. Additionally, Kaz is also revealed to have turned against Big Boss after learning of his true intentions and the fact that he abandoned him; he agreed to assist the Phantom and Big Boss's sons only because he felt that doing so would eventually contribute to Big Boss's downfall.
In a third, final secret mission, released in unfinished form on the collector's edition versions of the game as a video, Eli, since confirmed to be a clone of Big Boss, is seen to have occupied an island with his Metal Gear and released the last English strain parasites. Since it does not work on children, he has effectually created an isolated society with no adults. As Big Boss, wearing a gas mask, comes to return the children to the base, eradicate the parasites and take back Metal Gear, Cipher agents arrive, wanting Metal Gear for themselves. They are quickly annihilated by Eli piloting the mecha. In the end he is only subdued by the collective forces of the Diamond Dogs which the player has amassed throughout the game. After realizing Eli has entered puberty since and become infected by the parasite after all, Big Boss abandons him, ordering them to napalm the island on his departure. However, The Third Child appears and removes the parasite from within Eli, guiding him to safety. Eli vows to surpass his father as he departs with The Third Child, unaware that he has just been bested by a double.
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