Shadow Moses Incident

The night before the signing of the START III Accord, a nuclear weapons facility on Shadow Moses Island, off the coast of Alaska, was captured by Next-Generation Special Forces, led by members of FOXHOUND. Under the command of Liquid Snake, FOXHOUND and the NGSF formed the Sons of Big Boss, and initiated an armed revolt against the United States government. In addition, they also held hostages on the island, including the DARPA Chief Donald Anderson and ArmsTech President Kenneth Baker, both of whom also carried the PAL override codes.

Threatening the White House with a nuclear strike, the Sons of Big Boss demanded that the government hand over the remains of Big Boss, giving them a deadline of 24 hours. In addition, the Sons of Big Boss, to prove that they weren't bluffing about their capability of supplying a nuclear strike, also supplied the serial number to the US Government. The Genome Soldiers of the NGSF had been subject to advanced gene therapy, involving the use of Big Boss's "soldier genes" to enhance their combat skills and senses. Big Boss's DNA was considered to be a priceless treasure to the U.S. military, and the government could not allow it fall into the wrong hands.

"Introduction"
Approximately five hours later, by the request of Defense Secretary Jim Houseman, FOXHOUND's former commander Roy Campbell enlisted Solid Snake to help thwart the terrorist threat. Sending armed soldiers to Snake's retreat in Twin Lakes, he was later brought aboard the Ohio-class nuclear submarine USS Discovery, in the Bering Sea. Forced to strip down to his underwear, Campbell explained the situation to a reluctant Snake, while Naomi Hunter gave him an injection of nanomachines.

Campbell explained that they had discovered about sixty different kinds of "soldier genes," and that they cannot let them have Big Boss's body as it is considered far more dangerous than even a nuclear warhead. Campbell then explained that the President of the United States was the one who is supervising the mission, although he and his aides are still video conferencing instead of at the map room at Mount Washington's nuclear shelter, as they cannot issue a continuity of government until they can verify whether the Sons of Big Boss can possess the ability to launch a nuclear weapon, and that Defense Secretary Houseman is in operational control of the mission. In addition, Campbell also reveals that the NSA and the DIA are also involved in the mission, and that a nuclear specialist named Nastasha Romanenko will help Snake from her house in California. He also gave Snake a classified folder detailing their leader, Liquid Snake. After learning the info about the FOXHOUND members involved in the coup, they also explained that the Genome soldiers were involved, and that every member of the unit had inexplicably agreed to participate in the revolt. Snake also asked Campbell why he was involved in the mission, to which he replied that he simply wanted to take down FOXHOUND, but later admitted that it was because his niece, Meryl Silverburgh, a rookie soldier who had been called in as an emergency replacement, was among the hostages.

Afterwards, they persuaded him to infiltrate Shadow Moses in a solo covert operation. His objectives: Rescue the DARPA Chief Donald Anderson and President of ArmsTech Kenneth Baker and to find out if the terrorists had the ability to launch a nuclear strike and prevent them from doing so. Snake agreed under two conditions, that he doesn't take any orders from anyone besides Campbell, and that Campbell reveal all the details of the mission.

"Intruder"
A few hours later, Snake began to infiltrate Shadow Moses. In order to safely and undetectably arrive at Shadow Moses, the military had Snake delivered in an SDV (Swimmer Delivery Vehicle) to the island, due to the facility possessing Sonar detection capabilities that would alert the base to the presence of their sub, as well as negating the use of an air insertion (the latter of which also couldn't be performed anyway due to the weather). The U.S. military sent in two F-16 fighters from Galena AFB as a diversionary tactic. The plan was to begin the infiltration while the terrorists had their eyes on the F-16s. After successfully infiltrating the facility, Snake was contacted by Campbell and Naomi who reminded him of his mission objectives, and Mei Ling who explained to him how to use his Soliton Radar and Codec. He was also contacted by his old mentor, Master Miller, who explained to him that Roy Campbell told him about the situation, and that he volunteered to help as he felt he might be of some use. As soon as he arrived at the base, he watched the terrorist leader, Liquid Snake, board a Hind D gunship. Liquid used the Hind D to engage and shoot down the two F-16s.

Solid Snake then entered through the air ducts, which had been left open to be sprayed for rats. He then eavesdropped on a conversation between two Genome Soldiers where he learned that the DARPA Chief had been relocated, as well as the fact that another intruder had managed to sneak onto Shadow Moses Island and had killed three of the terrorists.

"Encounter"
Making his way deeper into the base, Snake easily achieved the first half of his first objective. He made his way into the prison cells where Donald Anderson, the DARPA Chief, was being held. Anderson informed Snake that the terrorists did indeed have the ability of a nuclear launch thanks to Metal Gear REX. Snake was shocked at the presence of Metal Gear, to which Anderson was shocked that Snake even knew about Metal Gear, as it was supposed to be one of their biggest top-secret projects. Snake explained that he had a few run-ins with them in the past. Snake then deduced that Anderson was on the island to oversee its development. Snake then mentioned that he heard that the project was supposed to be scrapped. Anderson revealed that it was never scrapped, and in fact it has already grown to be a joint venture between DARPA and ArmsTech and they were planning on doing live tests on it before it is sold for mass production. That is, before the revolutionaries came. Anderson informed him that the terrorists needed two codes to activate REX, one from himself, which the terrorists already had, and one from Kenneth Baker. Luckily for Snake, there were three PAL keys he could use to deactivate REX. Before Snake could escort the DARPA Chief to safety, Anderson suffered a heart attack and fell dead. Snake quickly contacted Campbell and it was clear Campbell knew more then he was letting on. As Snake made his way outside, he ran into Meryl, Campbell's niece. After having a brief conversion, they were ambushed by several Genome Soliders. After the coast was clear, Meryl ran into the elevator, shooting at Snake.

Snake, using information given to him by Anderson, headed to the basement to find Baker. Upon spotting Baker tied to a pillar rigged with C4, Snake feared he had arrived too late before being confronted by Revolver Ocelot, FOXHOUND's interrogation expert and ricochet genius. The two had a duel, before the intervention of the Cyborg Ninja who cut off Ocelot's hand, as well as cutting the wires holding Baker. 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. Afterwards, 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, disguised as a Genome Soldier, opened the door to the other building for him, allowing him to advance 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 a 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 easily put the tank out of commission by throwing grenades into the hatch after distracting its electronic sensors with a chaff grenade.

"Warhead Storage"
Entering into Dr. Emmerich's office, the Cyborg Ninja appeared once again and confronted Snake. Confused as to how the Ninja seemed to remember him, and finding his fighting style familiar, Snake defeated the Ninja, before he went crazy again. Snake realized the Ninja was Gray Fox, his old war buddy whom he had killed in Zanzibar Land.

Snake later revealed his discovery to Campbell, who was initially in disbelief until Naomi confirmed this as the truth. She explained that Gray Fox had been used for gene therapy experiments, led by FOXHOUND's former chief of medical staff Dr. Clark, who had died in a lab explosion two years prior. Campbell had been unaware of this, as it had happened shortly after his retirement from the unit; Naomi only knew about it because she had stumbled upon it when she joined FOXHOUND. She added that Dr. Clark had recovered the body of a soldier after the fall of Zanzibar Land, and revived him. He had then been outfitted with a prototype exoskeleton, treated with drugs, and experimented upon for four years, leading to the creation of the Genome Soldiers. Campbell was sickened by this, while Snake asked Naomi as to why she had failed to tell them sooner. She claimed that it was confidential information, but Snake suspected that there was more to it than she was letting on. When asked by Campbell as to what happened to Gray Fox afterwards, Naomi stated that he had died in the same lab explosion that killed Dr. Clark, at least according to reports. The Ninja's behavior led Snake to speculate that Gray Fox didn't even know his own identity, and that the only reason that he had lived on was for a fight to the death with Snake.

Rescuing Dr. Emmerich, who informed Snake he had developed Metal Gear REX, with no knowledge that it was to be nuclear-equipped. He believed that REX was intended for provide Theater Missile Defense against nuclear weapons. Dr. Emmerich informed Snake that REX's armament was handled by a separate department (in order to keep him in the dark) and that REX's rail gun (based on the rail gun for the SDI) was miniaturized for REX by a joint venture between ArmsTech and Livermore National Labs. Livermore Labs also developed an experimental nuclear weapon for REX. Finally, Emmerich warned Snake that if the PAL override keys didn't work, he would have no choice but to destroy REX. Snake also briefly expressed some concern for Hal Emmerich, due to his experience of Donald Anderson and Kenneth Baker dying from a heart attack shortly after telling him everything they knew.

"Mantis's Hymn"
Snake tracked down Meryl, but she only had one of the three detonation override keys on her. Heading to the REX hanger by way of the Communication Towers, Psycho Mantis took control of Meryl using his psychic powers. Snake had to knock Meryl out in order to save her. Snake proceeded to defeat Mantis who read both their minds, mentioning that he and Snake had a shared suffering, and predicting a great turmoil that awaited he and Meryl.

On their way to the towers, Sniper Wolf shot Meryl and used her as bait to lure Snake out. Snake, devastated, headed back to the armory to get a PSG-1 in order to battle Wolf. Finding one, he immediately headed back and managed to out-snipe Wolf. Snake was then captured and tortured by Ocelot who took the launch data Baker gave to Snake. Snake resisted the torture, knowing that if he gave in, Ocelot would kill Meryl.

In the cell, Snake encountered Anderson's corpse, but mysteriously it appeared he had been dead for days. He received a call from Naomi and Campbell and Snake learned more about the situation and a heated conversation between Campbell and Snake ensued. Snake realized that Campbell had hid information from him and that he knew that REX was a nuclear delivery system. According to Campbell, even the U.S. President had apparently been unaware of the existence of REX until the day before. To make matters more complicated, he was due to meet with the Russian President the following day for the formal signing of START III. If the fact that a new nuclear weapon was being developed by the United States were made public, there was a significant chance that the signing would never take place. Worse still, the loss of confidence in America's commitment to non-proliferation could create international turmoil. The government clearly had every reason to keep the situation under wraps, and there were ample indication that the terrorists had counted on the fact. The timing of this takeover as well as the twenty-four hour deadline said as much. And Naomi told Snake that the reason that U.S. Government couldn't hand over Big Boss' corpse to the terrorists is because the President passed a number of policies that severely restrict genetic engineering on humans and he couldn't afford to have the public know about the military's use of genetically-enhanced soldiers.

Eventually Otacon, using his stealth camouflage, helped Snake by giving him rations and ketchup. Thinking on his feet, Snake used the ketchup as fake blood and Johnny Sasaki, who was guarding him, foolishly opened the cell door to check on him, and Snake immediately capitalized on this opportunity. Knocking Johnny out, Snake escaped from the cell, heading back to the Communication Towers.

"Hind D"
Once atop the first tower, he encountered Liquid who was piloting the Hind D, who proceeded to shoot the bridge connecting to the second tower. Using a rope he found, Snake rappeled down to the lower bridge connecting to second tower. He met Otacon who attempted to fix the elevator while Snake headed back out to fight against Liquid in the Hind D. Snake shot down the Hind with stinger missiles and headed out the tower. Along the way, Otacon mentioned that the elevator started operating again, and he didn't even fix it. Snake boarded the elevator when Otacon called him again, realizing he forgot to tell Snake something he felt was important. There were five prototype stealth camouflage suits in his lab, counting his own. He was intending to get one for Snake, but when he went back to the lab, they were gone. He began to suspect that someone was "holding" the elevator down. Snake, slowly realizing what had happened, asked Otacon if the weight limit warning went off while he was on it. Otacon confirmed this, also finding it strange as he was nowhere near being over the weight limit. Snake asked him his weight, Otacon replying that he's 135 pounds, and the elevator's maximum limit is 650 pounds. Snake concluded that about five people would be required to go over the limit. Otacon realizing what had happened, attempted to warn Snake that whoever stole the remaining stealth camouflage prototypes were on the elevator with him. They then ambushed Snake at that moment, but Snake managed to defeat them. Emerging onto the snowfield, he was caught off guard by Sniper Wolf but he defeated her in the end. She told him about growing up and being taken away from the battlefield by a man named Saladin, who Snake correctly assumed was Big Boss. Now at peace, she requested Snake to "finish her quick." At that moment, Otacon turned up, admitting that he had fallen in love with her. Snake then shot Wolf before him and Otacon parted ways. Otacon promised that he would help Snake anyway he could.

"Colosseo"
Snake then headed to the control room where REX was being held and in the process met Vulcan Raven for the second time. Raven, armed with a gattling gun battled Snake and was eventually defeated. Raven revealed to him that the man he met in the cells who told him about Metal Gear was in fact, Decoy Octopus in disguise. Snake was then told by Master Miller that Naomi was not who she was making herself out to be. Based on information she gave earlier about her past, Miller made the deduction that she was lying and was most likely a spy. Snake mentioned that she did used to work for FOXHOUND, and Campbell then asked if she was involved in the uprising. Miller then hinted that she may actually be part of a third party, before telling Campbell to arrest Naomi, as she had endangered the operation. Miller then told Campbell that she needed to be interrogated to find out her employers, with Campbell worrying that they would be in big trouble if she turned out to be a spy. Snake then asked Campbell what he meant by that, to which Campbell quickly denied any meaning. Miller then asked Campbell if he was hiding anything that dealt with the mysterious circumstances of the DARPA Chief and the ArmsTech President's deaths. He then tried to reason with Miller to allow her to stay on the mission a little while longer, to which he accidentally let slip to Snake that he may have had some involvement in their deaths, with Snake remarking that he wouldn't give Campbell any more time.

"REX's Lair"
Making his way to the REX Hanger Control Room, Otacon contacted Snake and, after stating that he had overheard some guards talking about how REX's preparations were complete, revealed that he was in the computer room and thus could hack into President Baker's files to find the PAL key. He eventually contacted Snake after successfully hacking into Baker's computer files and stated that, although he hadn't found the PAL key file yet, he found out about what Metal Gear REX was capable of: Metal Gear REX was able to launch specifically-designed nuclear warheads with its railgun, and in fact the missiles it launched were stealth missiles, due to not requiring any fuel as well as being embued with stealth technology and a surface-piercing warhead, thus making it more apparent why the Sons of Big Boss would choose the START III signing date as their deadline: its development being exposed would, in the worse case scenario, result in the UN denouncing the United States and possibly even result in the President being brought down. Otacon also revealed that it was only simulated and thus never actually tested, explaining the exercise, and Otacon's analysis indicated that it accomplished more than they had hoped for, although he couldn't find the test data to back it up, with Snake grimly admitting that Baker gave him the test data, and that Ocelot took it from him during the torture. Otacon later contacted him telling him about the reason behind Baker's motives: ArmsTech was in a worse financial state than even Otacon thought, as there were rumors about a hostile takeover against ArmsTech after their X Plane project was scrapped by the military in addition to the funding cut caused by SDI, and that REX was their last chance at the company's survival, with Baker bribing the DARPA Chief to work on it. Snake overheard Liquid and Ocelot talking about their plans: instead of taking the superpowers head on (such as by launching a nuke against the United States or Russia), they would provoke the superpowers into fighting against each other, which would possibly result in mutual assured destruction. This was the reason why he went against Ocelot's suggestion to set the target for the nuclear strike to be Chernoton, Russia; preferring instead Lop Nor, China, the location of a nuclear test site. Firing a nuke on civilian territory would spell the end for any possible future negotiations, but an attack on a nuclear test site could still be concealed from the public by the Chinese government. This way, he could pit the Chinese (and also India, due to the CNTBT) against the U.S., and the latter would be forced to confess to some of its state secrets. At that point, he figured the other superpowers in the world would be interested in buying the system from them (Metal Gear REX and possibly improved Genome Soldiers), at which point he would sell them to the highest bidder.

They also mention that they have included more demands for the White House: one billion dollars, which, along with Big Boss's DNA, would be used to cure the Genome Soldiers from a mysterious genetic illness, and the FOXDIE vaccine. Not only that, but with Metal Gear REX in his possession, Liquid planned to join his forces (FOXHOUND and the Genome Army) with Sergei Gurlukovich's forces and turn Shadow Moses into Outer Heaven. With these vast resources at his command, Liquid would drag the world into the Third World War, wanting to fulfill Big Boss's dream of a world which always had a place for soldiers. Otacon contacted Snake, telling Snake he finally found the PAL Key file and discovered that the trick to the PAL Key was that it was made of a shape memory alloy that changed at different temperatures: room temperature, low temperature and high temperature.

"Enclosure"
Just then, Snake was discovered by Ocelot. Snake lost track of the PAL key after Ocelot shot it out of his hand. Snake was able to find the PAL key in the drainage ditch before being poisoned from the radiation. After having been taken into custody by Campbell, Naomi called Snake and told him that she was, in fact, a spy. She then went on to tell Snake why she did what she did, revealing that her brother was Frank Jaeger (better known as Gray Fox), which shocked Snake. He had adopted her in Rhodesia after her parents were killed. She had simply bought her identity of Naomi Hunter, and didn't even know her real name. It was after the Rhodesian Civil War that Big Boss had brought Frank and Naomi over to America, just before Big Boss and Frank went off again, to fight in the Mercenary War where Frank was nearly killed by Snake. Filled with pure hatred for Snake, Naomi joined FOXHOUND and waited for her time. She told Snake the shocking truth, he had been injected with FOXDIE, an artificial virus which targeted specific people and made their heart "commit suicide." He was injected with it so it could be used to kill off FOXHOUND and Baker, but Naomi reengineered the virus so that it would kill him too. However, she admitted that she doesn't hate him now, after learning his point of view on the fight with Gray Fox. She also told him that while she did hate him for crippling her brother (and thus indirectly putting him in gene therapy as a guinea pig), her hatred wasn't the primary reason why she injected him. Just before she could reveal the truth, Campbell wrestled her down and told Snake that he was forbidden to talk to her, but Snake was deeply upset at Campbell due to him being "betrayed and used" (he was especially upset about the FOXDIE part).

After Snake input all three PAL Keys, he was shocked to discover he had actually succeeded in activating Metal Gear. Just then, Snake was contacted by Master Miller. He thanked Snake for helping him. Miller revealed that Ocelot never input the detonation codes from Baker and Anderson. In fact, thanks to Anderson's death, they couldn't input all of the detonation codes as Anderson died before he could even reveal the codes, so they were forced to have Decoy Octopus pose as Anderson to try and trick Snake into getting the PAL keys, but they didn't anticipate that he would also carry FOXDIE. Campbell called Snake and told him that the person he was talking to wasn't Master Miller. He told him that the real Miller had been dead for three days which shocked Snake. In addition, although Campbell initially didn't know about Miller's death due to Miller's Codec being cut off from Campbell, Mei Ling also traced "Miller's" frequency from being within Shadow Moses. After the the truth came out, Miller revealed that he was actually Liquid Snake in disguise. Liquid trapped Snake in the control room and activated the soman gas valves, but Snake was able to easily escape after calling Otacon for help. After escaping, Snake finally confronted Liquid, face-to-face, and Liquid explained that he disguised himself as Miller in order to trick Snake more easily, and also revealed how the people who were using him as a disease vector were the people who recruited him: the Pentagon. Naomi was working with the Pentagon on making the virus program, although they did not anticipate that she would modify FOXDIE to target Snake out of revenge. He also explained that the reason the Pentagon decided to inject Snake with FOXDIE was so they could recover the Genome Soldier bodies as well as the Metal Gear REX weapon undamaged.

After explaining this to Snake, as well as briefly stating that he and Solid Snake are not ordinary twins, but twins that are clones of Big Boss as a result of the Les Enfants Terribles project, as well as expressing his hatred for both Solid Snake for receiving the dominant genes (making Snake "the dominant one"), and their father, Big Boss for apparently choosing Liquid knowingly to be the inferior one. Liquid told Snake that he wanted to kill Big Boss and exact revenge, berating his brother for "stealing that chance", as well as saying that by following Big Boss's legacy, he would "surpass and destroy [Big Boss]."

"Duel"
Liquid then climbed aboard REX, giving Snake no option but to destroy it. In addition, he also learned from Roy Campbell that if Snake failed to destroy REX, Campbell will be forced to resort to using the U.S.S. Discovery to bombard the Shadow Moses facility with nuclear warheads as a last resort. Otacon then called Snake and told him REX's weakness: REX's radome was Liquid's only view of the outside world while he was piloting it under the nigh-indestructible hull of the Metal Gear, meaning that he needed to destroy the radome to force Liquid to open up the cockpit and thus expose himself to enemy fire. Snake fought valiantly against REX but, it seemed like he was getting nowhere. At that point, Gray Fox jumped out from the shadows, damaging REX's radome in the process, temporarily blinding him. Fox and Snake hid, allowing Fox to explain that he adopted Naomi because he killed her parents, and felt guilty because of it. Fox then attempted to take out REX, but was eventually crushed under by it, although not before completely destroying REX's radome which forced Liquid to open up the cockpit and expose himself. With Liquid now being forced to leave REX's cockpit open, exposing himself, Snake shot REX several times with the stinger before REX exploded, knocking Snake unconscious.

Snake, hands bound, awoke atop the destroyed REX with Liquid watching over him, the latter having survived REX's destruction. Liquid proceeded to explain his plans to Snake, of creating a war-torn world in which warriors such as the two of them would always have a place, similar to Big Boss's dream. He also accused Snake himself of longing for such a world, despite his protests, citing his actions on Shadow Moses. Liquid went on to reveal the existence of "Les Enfants Terribles" to Snake, a project in which the two of them were created: They were both clones of Big Boss, with Liquid Snake having supposedly inherited Big Boss's "inferior" recessive traits, while Solid Snake inherited his "superior" dominant traits. The Genome Soldiers were also products of Big Boss's genes, though their gene therapy had resulted in the appearence of a certain genetic disease, for which they needed Big Boss's DNA to cure them. Liquid then revealed his belief that he was obeying the "will" of his genes, so that eventually he would surpass Big Boss and his own heritage, and that he would kill Snake in order to do so.

Liquid then directed Snake's attention behind him, to the prone body of Meryl, whom he had also placed atop REX. Although Liquid was unsure as to whether she was still alive, he told Snake that he would release her as soon as they both finished their business. Informing Snake that they were just about "out of time," Liquid relayed intel that the Pentagon had likely learned of Naomi's betrayal and REX's destruction, and were about to destroy the Shadow Moses facility. Apparently, Naomi's manipulation of the FOXDIE virus (casting grave doubts on the reliability of FOXDIE itself) and the destruction of REX (thus ending the nuclear threat) had put the Pentagon on alert. This was shortly confirmed by Campbell, who explained that a nuclear strike (from a payload of surface-piercing B61-13 tactical nuclear missiles) was on its way, though he intended to delay the launch in order to buy Snake and Meryl some time to escape. Campbell revealed that the Pentagon had deliberately and knowingly assigned her to Shadow Moses on the same day that FOXHOUND would rebel, in order to blackmail Campbell and that he was forced to hide vital information from Snake in order to ensure Meryl's safety. He apologized to Snake, saying that it was the least he could do for lying to him throughout the mission.

However, before he could give any orders, in order to confuse the chain of command, Campbell was arrested by Jim Houseman, the Secretary of Defense. Houseman personally took over as the mission's commander and headed for Shadow Moses on an E-3C AWACS. Houseman assured Snake that the facility would be destroyed, along with he and his brother, both of whom he considered to be an an embarassment from the 1970s. When Snake accused him of setting up Donald Anderson and the other hostages, he expressed sorrow that Anderson had died, due to the fact Anderson was a friend of his. Houseman then offered to stop the bombing if Snake provided him with the REX battle data. Since Ocelot had stolen it during the torture session, Snake couldn't meet that demand.

After Houseman signed off, Liquid demanded that the two fight. A gruelling bare-handed fight then ensued between the "Twin Snakes," with Solid Snake eventually forcing Liquid over the side of REX’s head, to a long fall to the ground below. Snake immediately ran to check on Meryl who was okay. Otacon called and Snake demanded that he leave as soon as possible, warning him about the F-117 Nighthawk and B-2 Spirit stealth bombers that were on their way to nuke the base, but Otacon refused. He told Snake that he would rather stay where he was and help him and Meryl to escape, using his hacking talents to open any doors and passages for them.

"Escape"
Snake and Meryl escaped through the adjacent supply route and commandeered a jeep nearby. With Meryl driving, and Snake manning the rear machine gun, they broke through several barricades along the supply tunnel, eliminating the Genome Soldiers they encountered along the way. Shortly thereafter, Liquid, having survived his previous fall, appeared in another jeep, pursuing them whilst opening fire with a FAMAS assault rifle. Snake and Liquid exchanged fire, until the two jeeps reached the end of the tunnel, and crashed into one another in the confusion of the chase. Snake and Meryl were trapped under their overturned jeep, as Liquid slowly approached. However, before he could shoot Snake he began to suffer from a heart attack, as a result of FOXDIE. Snake, now convinced that he too would die, remained solemn. He then noticed that the stealth bombers weren't present, despite the fact that they should have arrived by then. Snake then received a call from Colonel Campbell who informed the pair that Jim Houseman had been arrested, since he had managed to contact the President and inform him of what had happened: Apparently, Houseman was acting alone with the entire event. He also revealed that the air strike orders had been recinded and the six F-117s and B-2 bombers had returned to base, since Washington, D.C. was apparently not stupid enough to use nukes to cover up secrets (although Snake had some doubts about that). After learning that Meryl was alright, he again apologized to Snake for his behavior during the operation, though he also informed them that they were both now "officially dead," because their jeep had apparently crashed into the ocean. Snake requested a rescue for Otacon, and asked if he could speak to Naomi, who told Snake not to worry about FOXDIE and live his life as he would. Not afraid, Snake and Meryl rode off together into the Alaskan wilderness.

After the incident, the only surviving member of FOXHOUND, Revolver Ocelot, reported the events to the President of the United States, since he had actually been working as a double agent in order to recover REX's data. He revealed that he had purposefully killed the DARPA Chief because he knew of Ocelot's true identity and motives. He also reported that the "inferior" twin, Solid Snake had defeated his brother Liquid, the latter of whom died believing himself to be the inferior one. Ocelot then complimented the President on being a "well balanced individual", worthy of ruling the world, as the perfect clone of Big Boss: Solidus Snake.

Unconfirmed history
After sensing the black ops soldiers that had been sent to arrest him in Twin Lakes, Snake grabbed a 9mm Heckler & Koch P7 and bulletproof jacket to defend himself. Aiming his weapon at the soldier positioned outside his door, the group identified themselves as allies, under orders from Roy Campbell. Snake reluctantly lowered his machine pistol and raised his hands above his head. The soldiers then kicked down the door and pointed their assault rifles at him. After getting dressed, Snake was escorted aboard a transport helicopter and taken to the nuclear submarine Discovery.

At some point before the incident, Master Miller was doing his three-hour-per-day workout in his basement gym by punching his punching bag to take his mind off his reclusive living style since his retirement, when he heard one of his Huskies being silenced mid-howl. He grabbed a Glock handgun from behind a clipboard in his gym (he kept his main arsenal in another part of the house, but Miller kept a few guns in every room in the house), and prepared to investigate by going upstairs to check central alarm system control box, only to discover that his security system was cut. He then ducked behind some furniture in the hopes of catching the intruder by surprise, comparing the intruder's skills as similar to that of Solid Snake, as the intruder somehow managed to approach his house, on treacherous terrain, with the only road being covered by several feet of snow, and avoiding the security cameras from a mile away. Five minutes later, Miller detected nerve gas, and prepared to dress up in something warm fast, but could not reach the stairs to his escape hatch in the ice cave in time before he collapsed and succumbed to the nerve gas poisoning.

When Gray Fox first unveiled himself after Ocelot and Snake's battle, Naomi rushed to the bathroom in a fit of shock and trauma at seeing Gray Fox, but then reminded herself to calm down.

After Meryl opened the hangar door, she, while disguised as one of the Genome soldiers, boarded a transport truck that led to an alternate route to the warhead storage building. In addition, shortly before Snake arrived to fight Vulcan Raven, Raven surveyed the canyon from a glacier above, and wondered why the United States government would choose Shadow Moses, a reclusive and harsh island close to Russia, as the place to develop Metal Gear REX.

Upon arrival at the nuclear warhead storage building, Solid Snake took a picture of the warheads for Nastasha Romanenko using the Codec's camera option.

Shortly before their demise at the hands of Gray Fox, the sergeant of the six-man Genome squad tasked with guarding Hal Emmerich until he made the necessary completions to REX felt satisfaction that the scientists were in their predicament, as he hated them due to them having the answers to everything and because they made the big money, although he personally felt Emmerich should be dead.

Johnny Sasaki ended up brainwashed by the Sons of Big Boss into becoming one of their soldiers after originally being one of the computer maintenance members.

After Ocelot shot the PAL key out of Snake's hand, Snake had to dive into the nuclear-waste contaminated ditch around REX's hangar, and had to find the key within a 20 minute mark before he ended up poisoned from exposure.

During Vulcan Raven's fight against Solid Snake, Raven was grazed in the ear with a sniper rifle by Snake (Snake intended to give a clean shot to the head, but one of Raven's crows interfered with the shot). Afterwards, he hit Raven with a grenade in a manner similar to a bowling ball, blowing a hole in one of the crates and damaging Raven in the process. The crate contained Claymore mines, to which Snake used as a booby trap by lacing it with C4, and then luring Vulcan Raven to attack by shooting down one of Raven's birds, and then remotely detonating them with the Codec as soon as he got into position, mortally wounding Raven.

Before Naomi contacted Snake with a spare Codec, she went through a brief interrogation and stalled them. she also thought Campbell was unaware that the interrogation was already finished.

Shortly before Snake inputted the blue PAL key, three Genome Space Seals in winter fatigues delivered two cases: a square shaped container containing grenades of both flashbang and fragmentation varieties, C4, and claymore mines, and a rectangular box that contained an ArmsTech-designed portable Stinger launcher system with three stinger missiles that were intended to be picked up by Liquid Snake in a few minutes. A third container also ended up stolen by an intruder (whether the intruder was Gray Fox or Snake was not specified). The soldiers were also less enthusiastic about Liquid Snake's goals than they were two days ago, and that some of the surviving soldiers left via snowmobiles. The soldiers also joked about giving the hostages a closed-circuit TV to see the report on their attack, although one of the soldiers didn't understand that they were joking and reminded them that they were in an underground bunker. Snake overheard this and reported it to Otacon, who recognized it as being near the tunnels leading to the parking garage, with one entrance being sealed off permanenty, and the second being underground at a location unknown to him.

Behind the scenes
The "Previous Story" section of Metal Gear Solid 2 explains that the U.S. Government denied any involvement with the Shadow Moses Incident. The official story of the incident was that, according to the U.S. Government, the takeover of Shadow Moses was the work of a radical right-wing group. Their demands for the release of group members incarcerated in federal penitentiaries were never met, and the incident was speedily resolved by the successful deployment of a commando unit.

In Metal Gear Solid, there is an alternate ending. If the player submits to Ocelot's torture, Snake will leave Shadow Moses with Otacon after finding Meryl dead atop REX. It was often debated which ending was canon, due to Meryl's absence in Metal Gear Solid 2. However, In the Darkness of Shadow Moses: The Unofficial Truth, which was included with Metal Gear Solid 2, suggested that Meryl had indeed survived. This was later confirmed by her appearance in Metal Gear Solid 4.

For unknown reasons, the container that contains Snake's equipment, during Snake's torture at the hands of Ocelot, has a warning label on the lid. This could possibly be due to Ocelot planting a timer bomb among his items.

In Metal Gear Solid, the cutscene which mentions another intruder killing three of the terrorists only appeared if the player had been spotted before entering the air ducts. This was changed in Twin Snakes.

The phone call between Ocelot and Solidus Snake was originally to have taken place against a completely black background, besides the subtitles. The addition of the of the words "Metal Gear Solid" was under the suggestion of one of the production team members.

Appearances

 * Metal Gear Solid/The Twin Snakes
 * Metal Gear Solid 2: Sons of Liberty (mentioned only)
 * Metal Gear Solid 4: Guns of the Patriots (mentioned only)