Encounter

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Making his way deeper into the base, Snake located the prison cells where DARPA Chief Donald Anderson was being held. Anderson informed Snake that the terrorists indeed had the ability to launch a nuclear strike thanks to Metal Gear REX, the existence of which shocked Snake. Anderson also explained that the terrorists needed two detonation codes to arm REX: one from himself, which the terrorists already had, and one from Kenneth Baker. Fortunately for Snake, there was a PAL system that he could use to deactivate REX, via three card keys. Before Snake could escort the DARPA Chief to safety, Anderson suffered a heart attack and fell dead. After reporting to Campbell, Snake became suspicious that he knew more than he was letting on, but was unable to learn more.

Several heavy weapon Genome Soldiers prepare to ambush the holding cells.

Hearing the commotion from the next cell, Meryl Silverburgh effected her own escape, tricking the guard on patrol and stealing his uniform. As Snake made his way outside, he ran into the disguised Meryl, who held him at gunpoint. Following a tense showdown, they were soon ambushed by a squad of heavily armed Genome Soldiers, and the two joined forces to defeat them. After the coast was clear, Meryl ran into an elevator, shooting at Snake after falling under the influence of FOXHOUND's psychic, Psycho Mantis. Snake, using information given to him by Anderson, then headed to the lower levels to find President Baker. Upon spotting Baker tied to a pillar rigged with C4, Snake feared he had arrived too late before being confronted by FOXHOUND member Revolver Ocelot. The two had a gun duel, before the intervention of the Cyborg Ninja who cut off Ocelot's hand, as well as cutting the wires holding Baker, the latter also recognizing the Ninja upon seeing it.

The Ninja then vanished and Ocelot ran off, carrying his severed hand. Snake helped Baker, who mentioned that Meryl had the PAL override keys. He gave Snake a hint to where to find her Codec frequency. After he gave Snake the REX launch data, and telling him where to find Dr. Hal Emmerich, Baker revealed that he had been colluding with the DARPA Chief, Donald Anderson to secretly develop a new Metal Gear on the government's so-called black budget. For several years, regular payments in the tens of thousands of dollars had been made to the cooperate account of a dummy company for which Anderson's wife ostensibly acted as a consultant. After supplying Snake with an optical disc containing all the information on the Metal Gear project remaining (as the hard drive was shot up during the revolt), Baker was then questioned about his knowledge on the Ninja. Baker then told him that the Ninja was "FOXHOUND's dirty secret," before imploring Snake to stop Metal Gear's launch, as his company would be finished if its development were leaked. Snake, surprised at his statement, asked Baker if Metal Gear used currently-existing technology. Baker confirmed that the Metal Gear unit itself carried currently existing technology, but was unable to elaborate more: Baker began to suffer from a heart attack, eerily similar to the way in which Anderson died. Baker then rambled on about how the Pentagon had double-crossed him, before eventually dying. Snake then contacted Meryl and she opened the hangar's cargo doors for him, allowing him to advance north and find Dr. Emmerich. On his way there, Snake got a call from an anonymous tipster calling himself "Deepthroat" saying that he was "one of his fans." He warned Snake of claymore mines that had been planted nearby and that an M1 tank was waiting for him up ahead. Sure enough, he was confronted by the tank, commanded by Vulcan Raven and crewed by two Genome Soldiers. Snake put the tank out of commission by throwing grenades into the hatch after distracting its electronic sensors with a chaff grenade.

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