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Storyline:
In 2005 (six years after the events of Metal Gear 2)Foxhound and the genetically-enhanced Next-Generation Special Forces unit lead an armed uprising at Shadow Moses, a remote isle located in Alaska's Fox Archipelago and the site of a nuclear weapons disposal facility. In the Process they acquire Metal Gear REX a nuclear-capable bipedal tank, threatening the U.S. government with a nuclear reprisal if they do not receive a large cash ransom and the remains of the "legendary mercenary" Big Boss. Solid Snake in retirement at Alaska's Twin Lakes, is forceably dispatched at the request of Colonel Roy Campbell to penetrate the terrorist defenses and neutralize the threat.
Snake first locates hostage Donald Anderson, the DARPA chief. After he informs Snake of Metal Gear REX's deactivation procedure, he mysteriously dies of what appears to be a heart attack. Following a brief encounter with Meryl Silverburgh, who aids their escape from the base prison, Snake continues on to find the other hostage, Arms-Tech president Kenneth Baker. He is used as bait by Revolver Ocelot, and Snake is challenged to a gunfight, interrupted by the arrival of a mysterious cyborg ninja who severs Ocelot's arm before escaping. Snake is again briefed on the Metal Gear project by Baker; much like the DARPA Chief, he dies of a sudden heart attack just before revealing key information. Snake then contacts Meryl via Codec, and agrees to meet her in the base's warhead disposal area on the condition he contact Metal Gear's designer, Hal "Otacon" Emmerich. While searching for him, he encounters the giant Vulcan Raven in an M1 Abrams tank. He swiftly defeats him, and locates Otaocn in his lab.
The Cyborg Ninja Snake previously encountered reappears, and after a hand-to-hand battle reveals himself to be Solid Snake's former allie Gray Fox, who Snake believed he had killed years earlier. Before they can settle their score, the ninja vanishes again. Otacon, while safe, is unaware that Metal Gear is to be used as a nuclear delivery system, and breaks down when Snake informs him that he is continuing his family's close involvement with the US nuclear program. He agrees to aid Snake remotely, using special camouflage to procure information and supplies while remaining unseen. After which Snake meets Meryl, and they discuss their different roles as soldiers. Meryl having joined the military to feel closer to her father, an army officer killed in action. ultimately he allows her to accompany him on his mission.
As Snake moves on he encounters Psycho Mantis, which can predict Snake's movements and uses his powers to attack Snake. After defeating, and heading down a secret passage, Sniper Wolf ambushes them, wounding and capturing Meryl and eventually Snake following a sniper's duel. She hands Snake over to Ocelot, who tortures him, but Snake quickly escapes.
After being chased to the top of the base's communications tower, he encounters Liquid again, in a Hind-D attack helicopter. Despite being out-gunned, Snake shoots it down and upon descending the tower is yet again ambushed by Sniper Wolf. He kills her following a second duel. Otacon being enamored with her, is overcome with grief, but continues to assist Snake. Snake descends into the bowels of the Shadow Moses facility, first cutting through the base forge then down into the warehouses below.
Now Snake encounters Raven once again, this time face-to-face. After a long battle Snake managed to kills him. Before he dies, Raven reveals that the DARPA Chief who Snake encountered was actually FOXHOUND member Decoy Octopus in disguise.
Shortly after, Master Miller calls and reveals that Dr Naomi Hunter, a support agent, had given Solid Snake the genetically engineered virus "FoxDie" during his mission preparations, and is sending coded messages into the facility. Campbell swiftly orders her arrest. The virus, designed to kill people with particular genetic markers via cardiac arrest, which is responsible for the deaths of Octopus and the Armstech President. Naomi, struck by guilt contacts Snake in secret and confesses that she joined the mission to sabotage it, as she is the adoptive sister of the now barely human Gray Fox. However, upon learning of Snake's own tragic past through the current mission. She no longer has the heart to kill him directly, having reprogrammed the virus.
After infiltrating Metal Gear's hanger and following the supposed procedure to disarm the warhead. Snake unknowingly activates Metal Gear REX, after which Master Miller reveals himself to be Liquid in disguise. He informs Snake that his entire mission was manipulated by the renegades to allow the launch of the nuclear weapon. As a parting gift Liquid explains that they are the product of the 1971 Les Enfants Terribles project, a government sponsored effort to clone legendary mercenary Big Boss. However, part of the process requires that their genes be altered, Solid receiving all of Big Boss' dominant genes, and Liquid receiving all the recessive genes.
Drawn into battle with Metal Gear REX, Snake manages to disable the machine's sensors with the aid of Otacon, and Gray Fox manages to damage it further, but is wounded and crushed by its foot. REX is destroyed, but Liquid survives. Challenging Snake to a final fist fight atop Metal Gear, where Snake succeeds and is reunited with Meryl. Possibly for the final time, depending on the player's actions.After a protracted jeep-chase with the seemingly un-killable Liquid, Snake finally escapes the facility, and his brother collapses, killed by Foxdie. Colonel Campbell, calls off a nuclear air strike intended to obliterate the evidence of the day's events, and officially declares Snake killed in action to prevent the US Government returning for him in the future.
In the immediate aftermath, the player finds out Snake is actually genetically inferior to Liquid and has a longer amount of time left before Foxdie kills him.
There are two endings to this game. If you do not submit to Ocelots Torture Snake and Meryl will escape on a snowmobile while Otacon stays behind. The bonus item from this ending is the Bandana. If you submit to Ocelot's torture he will kill Meryl and you will escape with Otacon on a snowmobile and receive Stealth Camouflage. The official one is escaping with Meryl.
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