A great deal of time had passed since the legendary Solid Snake had killed Big Boss, the greatest soldier in the world, at Zanzibar Land. Snake had infiltrated the Zanzibar base and had ultimately eliminated the global threat posed by Big Boss and his band of soldiers. During the mission, Snake had also destroyed the revolutionary bipedal tank known as Metal Gear, a machine unmatched among military technology all over the world. Following his success, Snake retired to Alaska. However, the chilling and eerie possibility that Big Boss may have been his father haunted him for many years to come.
The year was 2005, six long revolutions after the Zanzibar incident. Snake awoke in his Alaskan cabin to the faint and distant sound of footsteps. He quietly made his way to the window and peered outside; in the darkness, he could see several heavily armed soldiers advancing on his home. Snake took hold of his gun and gripped it tightly, preparing for the firefight that would undeniably transpire within the coming moments. Unfortunately, the soldiers quickly surrounded his cabin, rendering resistance futile, and Snake was left with no option but to surrender. The unknown group of armed men took him to the USS Discovery, an Ohio Class Submarine. Aboard the craft, Snake found himself strip-searched and confined within a small room without even the slightest idea of what was going on.
After a few moments, the door finally opened. Roy Campbell, an ex-colonel of FOXHOUND who had worked with Snake during the Zanzibar incident, entered the room along with Dr. Naomi Hunter, an affiliate of FOXHOUND's medical staff. Campbell informed Snake of the circumstances surrounding his confinement: a certain irrepressible division of Special Operations Unit FOXHOUND, as well as members of the Next Generation Special Forces, had seized control of a nuclear disposal facility on Shadow Moses Island in Alaska's Fox Archipelago. They had taken hostages and demanded that the government turn over the remains of Big Boss. Failure to comply within twenty-four hours would result in the launch of a nuclear weapon. It was not until after Colonel Campbell revealed a picture of the terrorist leader that Snake agreed to take up the mission, for the man behind the takeover was none other than Liquid Snake: the individual with the same codename as Solid Snake, himself.
Snake infiltrated Shadow Moses Island and began his new mission. Soon after the commencement of the operation, he discovered that a new model of Metal Gear, the same bipedal tank he had faced in year's past, was secretly under development on the base. Additionally, something was apparently amidst the dark chambers of the island, as evident by Snake's horribly failed attempts to free the high profile hostages in confinement: the ArmsTech President, Kenneth Baker, and the DARPA Chief, Donald Anderson. During both disastrous rescues, the two men suffered nearly identical deaths from symptoms that suggested an abrupt heart failure. As the unnerving operation wore on, Snake located Hal "Otacon" Emmerich, the primary engineer in the Metal Gear "REX" project, the codename for the new model of terror. However, Otacon had already gotten himself into a bind: he was in conflict with a warrior Snake had previously encountered prior to Kenneth Baker's death, an intruder fitted in an exoskeleton that resembled a cyborg ninja, of sorts.
After a grueling hand-to-hand battle in the labs, Snake managed to defeat the fearsome ninja. Yet, the poignant recurrences of the ninja's words during the battle seemed to bewilder him, for the mysterious individual appeared to speak as if he had known Snake in the past. Shocked, Snake informed Campbell that he believed that the ninja was none other than Grey Fox, Snake's former best friend. He had battled and killed Grey Fox at Zanzibar solely due to the political climate of the times that put them at different ends of a heated conflict. Dr. Naomi Hunter commented that Dr. Emmett Clark, her predecessor, might have had something to do with Fox's presumed resurrection; then again, Clark had died in a lab accident several years prior to the Shadow Moses incident. Campbell assertively claimed that the probability of the ninja actually being Grey Fox was nonexistent, but Snake was convinced.
Following Snake's uncanny discovery, he went to Otacon, who explained the Metal Gear REX project and, more importantly, REX's location in the Underground Maintenance Base to the north. As Snake proceeded, he also met Roy Campbell's niece, Meryl Silverburgh, who had been stationed at the facility before its takeover. The two quickly found themselves falling in love with each other. Meryl handed Snake a PAL card, an emergency key that could supposedly override Metal Gear's detonation code, and, ergo, eliminate the threat. The two traveled together toward the Underground Maintenance Base, but they were hastily split apart by the sniper fire of FOXHOUND's sharpshooter, Sniper Wolf. Wolf shot an exposed Meryl in an attempt to lure Snake out from hiding, and the terrorists eventually captured him, as well as his brutally wounded ally.
During Snake's imprisonment, Revolver Ocelot, Liquid Snake's right-hand man, forced Snake through a grueling interrogation. Snake was left with a chilling decision between the safety of himself and Meryl. If he was to submit to the torture, Ocelot would take her life. Snake persevered through the severe torture and, with the aid of Otacon, escaped confinement and headed toward Metal Gear REX's dark and unsettling chamber. However, during this time, several distressing twists took place. Master McDonnell Miller, the mission analyst assigned to both the Zanzibar and Shadow Moses operations, reported that Naomi Hunter was actually a traitor, possibly in league with the terrorists. Miller dug further around and found evidence of a newly developed experimental assassination weapon in the Pentagon, one that Snake may have been injected with along with the multitude of standardized vaccinations during his mission briefing. The weapon targeted only specific people and eradicated its victims in a manner that simulated a heart attack. The Pentagon trump card, called FoxDie, was later discovered to be the cause of the ArmsTech President and DARPA Chief's deaths. Colonel Campbell immediately placed Naomi under arrest after finding she was sending coded transmissions to the Alaskan base.
As Snake approached the Underground Maintenance Base, Naomi managed to come into contact with him. She confirmed that she had injected Snake with FoxDie as an act of revenge for what he had done at Zanzibar Land: killing Frank Jaeger, also known as Grey Fox. Snake was perplexed at Naomi's affiliation with Jaeger, but his confusion was abruptly cleared when he realized that Fox was Naomi's brother. Snake understood Naomi's motives of vengeance and told her that he did not blame her for wanting him dead, but his feelings drastically differed when Naomi suggested that Snake's injection of the FoxDie virus was also a facet to the entire operation. Before she could clarify further, though, Campbell placed her back under arrest. Snake demanded an explanation, but the colonel was anything but responsive.
As Snake approached REX's chamber, he discovered the secret to deactivating Metal Gear. Apparently, the PAL card Meryl had given him was crafted out a shape-memory alloy. It acted as all three keys in one, altering shape at differing temperatures. Snake heated and cooled the card, accordingly, and entered all three keys into the emergency system. However, instead of deactivating, Metal Gear was actually activated. Snake had been set up all along. Within moments, Master Miller contacted the confounded warrior and confirmed that he, indeed, had acted as a pawn throughout the mission. Snake muttered in vehement anger as Miller revealed himself to be none other than Snake's very brother, Liquid Snake. Campbell quickly called Snake in an attempt to inform him that Master McDonnell Miller had been found rotting away in the confinement of his home, and that Liquid had assumed his identity for the Shadow Moses operation.
Liquid revealed that the DARPA Chief, Donald Anderson, had been inadvertently killed by Ocelot's sadistic interrogation prior to Snake's arrival at the island. Ergo, the man Snake had attempted to free in his first hours on the base was actually a terrorist member in disguise. The ploy, Liquid stated, played to perfection, further deluding the FOXHOUND operative with the illusory untruth that the use of the PAL keys was his sole and final option, for the keys acted as a reversible input: if the nuclear launch code had already been entered, the keys would disengage Metal Gear. If the code had not been entered, the keys would, instead, activate the bipedal nightmare on Earth. According to Liquid, the terrorists had not been able to figure out the DARPA Chief's launch code before his death, so they had turned to Snake to do the work for them.
Snake rushed out of the control room after Liquid and confronted him in front of Metal Gear REX. To Snake's horror, the chilling veracity that had plagued his mind since the Zanzibar incident unfolded into an irrefutable certainty: he and Liquid were, indeed, clones of their father, Big Boss, genetically created in a project titled "Les Enfants Terribles" or "the terrible children." Snake had inherited all of the dominant genes, while Liquid had received all of the recessive ones. However, veiled from this truth, Liquid was led to believe that because he, himself, had been the "recessive" clone, he was equally inferior. And, for this, he sought revenge. Interestingly, it was later uncovered that the so-called soldier gene, the series of genes discovered in 1999 that defined an individual's biological capability as a warrior, was expressed recessively. So, while Solid Snake had been genetically dominant, this actually resulted in his inferiority as a warrior.
After proclaiming his fury, Liquid leapt into REX and activated the demonic weapon that would undoubtedly drag the world into the twenty-first century. To his horror, Snake watched as REX sprung to life. Just as in the past, Snake battled Metal Gear in an epic struggle of good versus evil.
As Snake began to fall to the enormous machine of death, Liquid attempted to crush him under REX's weight. Grey Fox reappeared and saved Snake with only seconds to spare. The two old friends found themselves caught up in one final exchange before the end. Fox leapt away toward Metal Gear, evading the bullets that seemed to rain down upon him by the hundreds, and fervently clashed with the weapon of terror in a fiery attempt to bring REX's radar, the Radome, to ashes. Snake beheld the scene in trepidation as he watched Metal Gear impale the man from Zanzibar into the wall. The lifeless Fox gazed out upon the Radome, and in a concluding act of desperation, he brought his weapon into the air with the last ounces of strength in his body and fired.
The Radome erupted into flames as REX stumbled backward; Fox collapsed onto the bloody concrete beneath him. Jaeger glanced to the side through his red-glazed eyes toward Snake and muttered through his gritted teeth: "Snake: we're not just tools of the government, or anyone else! Fighting was the only thing...the only thing I was good at. But at least I always fought for what I believed in. Snake... farewell. Snake screamed Fox's name as Metal Gear crushed the valiant man below its colossal mass.
"You see? You can't protect anyone! Not even yourself!"
Liquid's words echoed hauntingly within the underground chamber. Snake, fueled by his unparalleled rage over the death of the man who had saved his life, launched a final Stinger missile into the mouth of REX. The behemoth exploded in a brilliant light and sent Snake flying into a wall, knocking him unconscious, but not before he heard what sounded like footsteps nearing him.
When Snake came to, he found himself atop the wreckage of Metal Gear; before him, Liquid Snake stood in wait. The brother of light and the brother of dark conversed for what seemed like hours. Liquid revealed his true intentions for reestablishing Big Boss's dream: he wanted to recreate and fashion a world where soldiers would be revered, honored, and, above all, needed, as they once were. Colonel Campbell quickly contacted Snake and warned him of a completely new peril: the Pentagon had received word that the terrorist threat had been eliminated, and in an effort to eradicate the truth of what had truly occurred, they would launch the entire facility into nuclear inferno. In an attempt to redeem himself for all of the lies he had told, Campbell planned on issuing an order to stop the launch, ergo disrupting the chain of command and buying Snake ample time to escape the island.
This plan would not unfold, however, as the colonel was placed under arrest by the Secretary of Defense, Jim Houseman, who had orchestrated the Metal Gear black project. Houseman, out of sheer arrogance and malevolence, enlightened Snake of the true nature of the operation: from the beginning, Snake was simply being used as the vector to spread FoxDie. By coming into contact with the terrorists, everyone on the base would be subjected to the virus, and, consequently, to their ultimate demise. Following the horrid epidemic, the government would steal Metal Gear, as opposed to destroying it. Since REX had been destroyed, Houseman intended to evaporate any evidence of what really happened there, even if it meant a nuclear strike.
Liquid chuckled at his inevitable fate as he gestured behind the daunted soldier and Snake turned to see Meryl, lying unconscious. Beside her, a small nuclear module began to count down from two hundred seconds. Almost mocking the circumstances that surrounded the conflict, Liquid remarked that she would make for a perfect sacrifice for their final battle. Snake grimaced, and the clash of the titans began in a battle built upon antagonism and resentment. In the end, Snake launched Liquid from the head of Metal Gear REX to his apparent death. With only a few seconds to spare, Snake deactivated the bomb and untied Meryl and to his utter amazement and relief, Meryl had somehow survived. Snake contacted Otacon and informed him of the impending nuclear attack, advising him to escape while he still could. Otacon, having undergone a radical change of character, refused to leave and promised Snake he would clear a path for the two to escape.
Snake and Meryl descended from Metal Gear, hopped into a nearby jeep, and rushed toward the exit of the facility, gunning down any guards along the way. Ironically, their escape would not go unhindered, as a second jeep advanced on them from behind: Liquid. The two brothers linked by cursed genes engaged in a firefight as they sped down the tunnel, and neither individual seemed to gain the upper hand. The climatic chase came to an abrupt halt as the two vehicles crashed at the end of the tunnel. Snake and Meryl managed to survive, yet were both caught underneath their overturned jeep. However, the same did not hold true for Liquid; he stumbled forward, fueled by nothing other than his vehement detestation for his clone brother. He raised his gun and trained its sights between the eyes of Solid Snake.
Liquid collapsed into the snow, dead, as he fell victim to the FoxDie virus.
After the two freed themselves from underneath the wreckage, Colonel Campbell called Snake via the Codec and notified him that the President had called off the bombing, as the Secretary of Defense had been acting alone the entire time. In addition, there was a snowmobile nearby that could take them to Fox Island, where an evacuation helicopter awaited. Shortly thereafter, Naomi spoke with Snake, having been released from custody. She verified that she truly did not know when or where FoxDie would end his life. Snake would later find out that Naomi had tampered with the virus before it was implemented into the operation, programming it to strike at a random time. The expansion upon his life was a gift, he thought, one that deserved to be spent with purpose. Meryl and Snake departed from Shadow Moses and disappeared into the Alaskan wilderness.
Following the Shadow Moses incident, the two survivors most likely had a relationship. Otacon, who survived the endeavor, contacted Snake a few weeks after the operation. According to him, Revolver Ocelot, the sole terrorist survivor, had sold Metal Gear's data on the black market, and numerous countries would soon develop their own versions of Metal Gear all over the world. Otacon convinced Snake that he could make a difference and persuaded him to join in forming a new group, Philanthropy, an anti-Metal Gear organization officially recognized by the United Nations. For the next two years or so, Otacon and Snake destroyed dozens of rogue Metal Gears around the globe.
-- Summary by Grant Gordin, Metal Gear Solid: The Unofficial Site