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 rebelled against the United States government, led by members of FOXHOUND, under the command of Liquid Snake. Together, FOXHOUND and the NGSF 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 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
Requested by Secretary of Defense Jim Houseman, Colonel Roy Campbell, former commander of FOXHOUND, sent assault rifle-armed black ops soldiers to Solid Snake's retreat at Twin Lakes. Snake, after sensing them outside, prepared to arm and defend himself with a 9mm Heckler & Koch P7 and a bulletproof jacket. He was preparing to fire at the soldier positioned outside of his bedroom door until the group identified themselves as allies, and were to "arrest" Snake, under orders from Campbell. Initially confused at to why his former C.O. would do something as awkward as this, he reluctantly lowered his machine pistol, and was ordered to raise his hands above his head and not move. After obeying, the soldiers kicked down the already unlocked bedroom door and pointed their rifles at Snake. After getting dressed, he irritably hoped that Campbell had a very good reason for the method he chose in summoning him from retirement. After boarding the transport helicopter, Snake ended up on the submarine USS Discovery in the Bering Sea.

After being forced to strip down to his underwear in the bowels of the sub, Campbell explained the Shadow Moses situation to Snake, and then Naomi Hunter entered the room to give him an injection of nanomachines. 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 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 Snake knew better, and asked the real reason. Campbell 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. 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 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 reveals 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 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 began to suffer from a heart attack, eerily similar to the way in which Anderson died. Baker then rambled 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 Rivermore National Labs. Finally, Emmerich warned Snake that if the PAL override keys didn't work, he would have no choice but to destroy 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.

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, Snake overheard Liquid and Ocelot talking about their plans: To provoke the superpowers into fighting against each other rather than taking them head on (such as: By 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 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, 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, 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 had made an edit to its programming before injecting it into Snake, which meant 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. 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 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. 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 certain mutations, 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 REX's destruction and were about to destroy the Shadow Moses facility. This was shortly confirmed by Campbell, who explained that a nuclear strike was on its way, though he intended to delay the launch in order to buy Snake and Meryl some time to escape. He apologized to Snake, saying that it was the least he could do for lying to him throughout the mission, and that he was forced to hide vital information from Snake in order to ensure Meryl's safety. It turned out 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.

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 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, who 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 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 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.

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.