Shadow Moses Incident

The night before the START III was to be signed, during a routine FOXHOUND training mission at Shadow Moses, a nuclear weapons facility on a remote island off the coast of Alaska, the Next-Generation Special Forces unit rebelled against the United States government, led by members of FOXHOUND, under the command of Liquid Snake. Together, FOXHOUND and the Next-Generation Special Forces formed the Sons of Big Boss terrorist group.

Threatening the White House with a nuclear strike, the Sons of Big Boss had one demand: the body of the greatest soldier who ever lived, Big Boss. The Next-Generation Special Forces (also known as the Genome Army), already the subject of advanced gene therapy, could use the genes of Big Boss to make themselves the ultimate soldiers. The government couldn't let this happen.

Requested by Secretary of Defense Jim Houseman, Colonel Roy Campbell, former commander of FOXHOUND, had sent soldiers who were apparently assault rifle-armed black ops to Solid Snake's retreat at Twin Lakes, and Snake, sensing them outside, prepared to arm and defend himself with a 9-mm Heckler & Koch P7 and a bulletproof jacket. He was going to fire at the black ops positioned outside of his bedroom door when they identified themselves as allies, and were under orders from Campbell to "arrest", in actuality, summon Snake out of retirement. Initially confused at why Campbell would do something as awkward as this, he reluctantly lowered the machine pistol on the table. Afterwards, they told Snake to raise his hands above his head and not move. After obeying, the soldiers kicked down the already unlocked bedroom door and pointed the rifles at Snake. After getting dressed, he irritably hoped that Campbell had a very good reason for the method he chose in summoning him. After boarding the transport helicopter, Snake ended up on the Submarine USS Discovery at the Bering Sea.

After being forced to strip down to his underwear in the bowels of the ship, Campbell explained the situation to Snake, and then Naomi Hunter entered the room to give him a shot. Campbell explained that they had discovered about sixty different kinds of "soldier genes", and 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 at least most of the soldiers were possessed by Psycho Mantis. Snake also asked Campbell why he's involved in the mission. At first it seemed like he wanted to take down FOXHOUND, but Snake knew better, and asked the real reason. Campbell later admitted that it's because his niece, Meryl Silverburgh, a FOXHOUND rookie who was called in as an emergency backup, 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.

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 UDV (Underwater Delivery Vehicle) to the island.

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. As soon as he arrived at the base, he noticed Liquid starting to board a Hind D gunship. Liquid Snake used the Hind D helicopter to engage and shoot down the two F-16s.

Solid Snake then entered through the air ducts, which were left open to be sprayed for rats. He also eavesdropped on a conversation between two Genome Soldiers where he learned that the DARPA Chief was relocated, as well as the fact that an intruder besides himself had managed to sneak onto Shadow Moses Island and killed three of the Sons of Big Boss members.



Discovery

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 and 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, the Chief suffered a heart attack and fell dead. Snake quickly contacted Campbell and it was clear Campbell knew more then he let on. As Snake made his way outside, he ran into Meryl, Campbell's niece. Before they could talk, they were ambushed by enemy 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 Kenneth 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 died of a heart attack, eerily similar to the way Anderson died. Before he died, Baked rambled about the Pentagon double-crossing him. 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 naming himself "Deepthroat" saying he was "one of his fans." He warned Snake of a tank up ahead. Sure enough, he was confronted by a tank being commanded by Vulcan Raven and crewed by three Genome Soldiers. Snake easily put the tank out of commission by throwing a grenade into the hatch after distracting it with a Chaff Grenade.

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. He later revealed this to Campbell, who was initially in disbelief until Naomi confirmed this as being true. She explained that Gray Fox was being used for the Gene Therapy experiments by Dr. Clark, FOXHOUND's medic and the same person behind the Genome Soldier project that was operated by FOXHOUND. Campbell denied any knowledge of this, to which Naomi explained that he didn't know because it happened shortly after he retired from the unit. In fact, she only knew about it because she stumbled upon it when she joined FOXHOUND. When Campbell asked her where Dr. Clark was, she responded that "he" died in a lab explosion two years prior. She also revealed that prior to the experiment, Dr. Clark had arranged for a clean up crew to find and deliver back to America a fallen soldier in Zanzibar Land, whom Snake correctly guessed was Gray Fox. She confirmed this as such and coldly tells Snake and Campbell that he was experimented on for four years, outfitted him with a prototype exoskeleton and that the Genome Army was spawned from these same experiments. She also revealed that to experiment on him, Dr. Clark and "his" staff kept him drugged. Campbell, horrified at this revelation, mentioned that this experiment was "the sickest thing he has ever heard." Snake then asked her as to why she failed to tell them sooner. She claimed that it was confidential information from the government, but Snake suspected that there was more to it than she's letting on. When asked by Campbell as to what happened to Gray Fox afterwards, Naomi stated that he died in the explosion, at least according to the reports. Campbell then asked why was Gray Fox the ninja, assuming that he was Gray Fox. Snake mentioned that he doubted that even Gray Fox knew, and he also seemed to not even know himself. Campbell then asked if he's living on was his will to fight. Snake suspected that this was the case, and that he cared for nothing more than a fight to the death with Snake, and that while he may not want to do it, he suspected that Gray Fox wanted it. Rescuing Dr. Emmerich, who informed Snake he developed Metal Gear REX, with no knowledge that it was to be nuclear-equipped, said that if the PAL Override keys didn't work, Snake would have no choice but to destroy Metal Gear REX.

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 receieved a call from Naomi and Campbell and Snake learned more about the situation and a heated conversation between Campbell and Snake ensued. 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.

Enclosure

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.

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 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, with Campbell saying she could be "one of their spies."

REX's Lair

Making his way to the REX Hanger Control Room, Snake overheard Liquid and Ocelot talking about their plans: to provoke the superpowers into fight against each other rather than taking them head on (such as: launching a nuke against the United States itself), which would most likely 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 against the US – 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' 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, having hacked into Baker's personal files, 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, Ice Cold Temperature and Intense Heat Temperature.

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 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 had made an edit to its programming before injecting it into Snake, which meant it would kill him too. However, she admitted that she now doesn't hate him, 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 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. After the the truth came out, Miller revealed that he was actually Liquid Snake in disguise. Liquid trapped Snake in the control room, but Snake was able to easily escape after calling Otacon for help. After escaping, Snake finally confronted Liquid, face-to-face, and Liquid explained about 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. 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 as well as the battle data undamaged.

After explaining to Snake this, 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 his (Big Boss') legacy, he would "surpass and destroy [Big Boss]."

Liquid then climbed aboard REX, giving Snake no option but to destroy it. 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.

Escape

Snake awoke atop the destroyed REX with Liquid, having survived REX's destruction watching over him. Liquid proceeded to explain his plans to Snake, about how he wanted to turn the world into a war zone where warriors such as him will always need a place, just like Big Boss's dream. Liquid also explained about the Les Enfants Terribles project, and how they were both created by it. Twin clones of Big Boss, Liquid received all the inferior genes while Solid received the superior. Liquid also told Snake that the Genome Soldiers are also products of Big Boss's genes. But they are a failure since they are dying due to a strange genetic illness, and that they need Big Boss's DNA to cure them.

Suddenly, Snake received a call from Campbell. A nuclear strike was on its way to Shadow Moses, but Campbell said that he would try to stop the launch, which would confuse the chain of command and buy Snake and Meryl some time to escape, saying that it was the least he could do for lying to him about the mission, and he also told Snake that he was forced to hide several pieces of vital information from Snake in order to ensure Meryl's safety. It turned out that the Pentagon had deliberately and knowingly chosen her assignment to Shadow Moses to be quidthe same day that FOXHOUND would rebel in order to blackmail Campbell. Before Campbell could give the order, he was arrested by Jim Houseman, the Secretary of Defense, who told Snake that a nuclear strike would destroy Shadow Moses, along with the twin snakes (which he considered an embarassment from the 1970s). When Snake accused him of setting up Anderson among the hostages, he stated that he actually did want Anderson to come back alive, as he was his friend. He offered to stop the bombing if Snake handed him the REX battle data. As Ocelot had stolen it during the torture session, he couldn't meet that demand. Liquid demanded that the two fight, with Snake eventually knocking Liquid over the side of REX’s cockpit, a devastating fall.

Snake immediately ran to check on Meryl who was okay. Otacon called and Snake demanded he leave as soon as possible, telling him that Stealth Bombers were on their way to nuke the base, but Otacon refused, saying he would rather stay where he was and help them escape using his hacking talents to open any doors and passages for them.

The Best Is Yet to Come

Snake and Meryl escapeed through the adjacent supply route and commandeer a jeep nearby. As they were making their escape Liquid, having survived the fall, appeared in another jeep, chasing them whilst shooting at them. Snake and Liquid shot at each other until they reached the end of the tunnel where the two jeeps crashed. Snake and Meryl were trapped under their jeep as Liquid slowly approached… but just before he could shoot Snake he fell dead because of FOXDIE. Snake, now convinced that if FOXDIE would kill Liquid it would kill him too, was solemn about what this meant. He then noticed that the Stealth Bombers weren't present, despite the fact that they were to bomb the place. Snake then received a call from Colonel Campbell who informed the pair that Jim Houseman was arrested, because of his contacting the President about what happened: Apparently, Houseman was acting alone with the entire event. He also revealed to Snake that both the nuclear strike and air strike orders were recinded and the F-117s and B-2 Bombers returned to the Galena Air Force Base, as Washington, D.C. was apparently not stupid enough to use Nukes to cover up its own secrets (although Snake has some doubts about that). After learning that Meryl was ok, he apologized to Snake for keeping those secrets to him before, and he also explained that they were both "officially dead" because their jeep 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 into the Alaskan Wilderness alone together. This event became known as the "Shadow Moses Incident."

It was later revealed that Snake was the genetically inferior twin, not Liquid. It also revealed that Ocelot was a double agent working for the President of the United States, and the President himself was the third Snake (Solidus). Ocelot was to steal the MO disc and deliver it to the President. He also killed Anderson because he knew Ocelot's true identity and motives.

Behind the Scenes
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.