San Hieronymo Incident

Six years after the events of "Operation Snake Eater," Naked Snake's former unit, FOX, broke their allegiance with the CIA and went renegade. Snake himself was targeted by the FOX Unit, which sent armed soldiers to attack and capture him.

Imprisonment

Exactly twelve hours later, Snake awoke in the San Hieronymo Peninsula, Colombia, where he was tortured by FOX's interrogation specialist, Lieutenant Cunningham. Cunningham attempted to locate the whereabouts of the missing half of the The Philosophers' Legacy, which had gone missing at the conclusion of Operation: Snake Eater. He explained that the United States Government had already acquired the other half of the Legacy from the Soviet Union and that they suspected Snake of having stolen the other half.

However, Snake managed to escape imprisonment with the help of fellow prisoner, Roy Campbell, the sole survivor of an American Green Beret team sent in to investigate the peninsula. Campbell, upon recognizing Snake as "Big Boss", commented that he had become a legend in the Black Ops world, and explained to him that the peninsula was the site of an abandoned Soviet missile silo. The Soviets had created the base in secret after helping the FARC rebels in 1964, after they failed to do so in Cuba during the Cuban Missile Crisis. However, the base construction plans had been abandoned due to détente, thus causing the SALT to limit each country's ballistic missile supply and eliminating the need for a new missile base. However, the base had recently become active again, prompting Campbell's Green Berets to investigate. However, The FOX Unit ambushed them and wiped them out, capturing Campbell. Snake attempted to free him, but his cell required a special key. Campbell tells Snake to go to the communications base to send out an SOS signal via an encrypted message that wouldn’t be traced.

Snake then attempted to contact his old commanding officer, Major Zero, but was instead greeted by his old FOX comrades Para-Medic and Sigint. They revealed that he and Zero were being accused of instigating the FOX revolt, as well as stealing a prototype weapon from the military a month ago. The only way for Snake to clear their names would be to find and apprehend the leader of the rebellion, whose identity was currently unknown. The FOX Unit had also complicated matters by bringing the remaining Red Army soldiers under their control. Sigint suggested that Snake try to accomplish the mission by recruiting some of the soldiers himself.

After returning to the detention center to free Campbell, he informed him of the situation. He also asked Campbell if he was willing to help, but he declines due to a broken leg and fever. Snake then asked him if he'd drive if they stole a truck, to which he agreed. The pair then reviewed what they should do first. According to Campbell's briefing, the Green Beret's first recon target was to be a Soviet patrol base. He knew where it was located, but not any other facilities of the base.

Snake proceeded to infiltrate the patrol base, where he overheard two soldiers discussing a weapon that was supposedly powerful enough to obliterate every major city in Russia. He managed to steal some secret documents, confirming that FOX was planning to use this secret weapon against Russia, and containing outline details of a launch plan. Snake was in disbelief, and that even if the launch plan was real, it was a bluff to strengthen their hand. In the end, he and Campbell were forced to assume that it was true and that it would spark a world crisis.

The fact that there were only two of them against both the Red Army and FOX didn't sit well with them. Campbell asked Snake if he noticed if any of the Red Army soldiers had negative thoughts about their commander, leading Campbell to decide that they should attempt to recruit the soldiers to their side. Snake agreed, deciding to find a potential recruit, and convince him to join their resistance. Campbell also informed Snake of the name of the FOX commander: Gene.

To Arms

Snake quickly captured a Soviet soldier, named Jonathan. Regaining consciousness, Jonathan attempted an escape by grabbing Campbell's pistol, but before he could shoot, Snake pinned him down. Complimenting him on his recovery and quick thinking, Snake introduced himself, telling him that he was just a soldier, neither with the Americans nor with FOX, and that they were here to stop the FOX rebellion. Their mission was to free the soldiers on the peninsula from Gene's control, and apprehend the traitors in the FOX unit. Campbell asked if he was willing to join, but Jonathan laughed at this, and informed the pair that they didn't rebel because Gene made them, but because their country had betrayed them. The Red Army soldiers had spent years on the peninsula without contact due to the secrecy of their mission, and without decent food in a harsh climate. Many had died, but they stayed believing their efforts to be for the good of Russia, but they were repaid by being "stabbed in the back". Campbell commented that if the existence of the base was revealed, Moscow's position in the SALT program would be compromised. However, Jonathan replied that his unit didn't care about political rationales, they were forced to stay, making it seem as though it was the work of a few out of control soldiers. They turned to Gene because he wanted to make a nation not of soldiers, but for them, and that they are loyal to Gene because of their belief that he will deliver them justice, and the only thing they feared is losing that justice. Snake told him that a professional soldier never brings justice to a mission, politics are fickle, and that the only ones who need a reason to fight are those who fight for a living. He cites The Boss's sacrifice as how he knows this. Jonathan, realizing that Snake is Big Boss, the hero who defeated Colonel Volgin at Groznyj Grad, is amazed, and finally decided to join them, not as a Red Army member, but as a soldier.

Afterwards, Campbell's condition worsened and they realized that he may have contracted malaria. The preventive drugs they had weren't working, so Snake sneaked back into the communications base to contact Para-Medic. She drew the conclusion that the malaria bug Campbell had may be of a type that the drugs had no effect on, but luckily one of the recruited soldiers knew the location of a hospital which had recently received a suspiciously large shipment. After making their way there they soon discovered the drugs had been used up, and the only thing that remained was a shipment of materials headed for a lab north of the hospital. Meanwhile, Cunningham had discovered that Snake and Campbell had escaped, and ordered a search team to find them. While he flew over the hospital by helicopter with other FOX personnel, a mysterious blonde woman noticed Snake from afar, forcing him to take cover. Tailing the chopper, they find the research lab where Snake’s group observed Cunningham and FOX commander Gene, along with the mysterious woman. Gene talked to the woman about the status of a soldier named Null. Suddenly, both sensed something was amiss, and their predictions proved correct as scaffolding that the soldiers were working on for a Heliport collapsed right in front of them. One soldier ended up injured and tried to apologize, though Gene forgave his error and had him sent to the hospital. He apologized to the other soldiers for making it seem as though the work was more important than the soldiers’ well being, and expressed that the age of soldiers being treated as tools was coming to an end.

Sneaking into the research lab proper, the mysterious woman Snake saw earlier discovered him in the room with a culture tank. After hiding him from other soldiers, she introduced herself as Elisa, with Snake asking if she was a member of FOX. She replied that she was simply a medic, and that it was her twin sister, Ursula, who was with FOX. She told Snake that Ursula was one of the most powerful psychics in all the Communist world. Snake asked Elisa about the soldier in the culture tank and she told him that this was Null, and that he was known as “The Perfect Soldier.” Incapable of emotions or doubts, the Perfect Soldier’s emotions would be reset after every mission and his senses honed to razor sharpness. Elisa handed Snake a package containing the treatment for the malaria, and telling him to head for the harbor to find what he was looking for. Before Snake left Elisa then warned him that if he ever saw Ursula in front of him, he should shoot. If he couldn't do that, he was already dead.

Diversionary Ops Now free from malaria, the group decided to set up a spy unit to find any leads that would lead them to the harbor. Sending units to the supply depot, they quickly discovered the location of a map detailing cargo shipment routes. The group’s sneaking unit retrieved the document which also revealed the locations of the town, rail bridge and the security base. However, Campbell discovered that the rail bridge that they needed to cross to reach the harbor, had been closed off and turned into a checkpoint. Snake decided that, instead of pushing through head on, it would be better to make diversions elsewhere: by blowing up enemy facilities or landmarks, forces would need to be pulled from the bridge in order to help out elsewhere. Snake snuck back into the supply depot to steal some TNT while the spy units located places within various facilities that, if destroyed, would cause a sufficient distraction: trucks in the supply depot and town; an armory in the Soviet patrol base; and the culture tank, used to house the Perfect Soldier, in the research lab. After destroying some of these targets, Snake and his unit headed to the rail bridge to cross to the other side of the peninsula.

Successfully infiltrating a cargo ship docked in the harbor, Snake observed a Soviet officer speaking to a man that he recognized: an old war buddy of his from Vietnam, codenamed Python, whom Snake had thought long thought dead. The drunken officer, Colonel Skowronski, was upset at Python for "touching his collection", and taking command of "his base". Python, however, was amused that Skowronski was in hiding, and couldn't even command his own unit anymore. Skowronski attempted to shoot him with his AK-47, but the bullets became frozen and halted before they could hit him. Skowronski screamed in horror, accusing Python of being a monster. Python took Skowronski’s gun in his hand and, froze it solid, using liquid nitrogen ejected from his special suit. He threw Scowronski into a cell and froze the lock. After Python left, Snake approached Skowronski, who explained that he had lost the chain of command to Gene, and with it, his entire platoon in the past four weeks. Gene was using greed and fear to get the soldiers to “dance to his tune.” Snake comments on the Lavotchkin La-5 that Skowronski had aboard the ship, who responded that if he had a MiG or a Sukhoi he would kill Gene, laughing maniacally. Snake shoots the ice lock on the cell, and continues on his mission.

Snake eventually finds a crate with US markings and deduces that this must be what they were looking for. However, most of the crates were empty, but some still had spare parts left behind, most notably: "HEAT rounds for a recoilless cannon, spare barrels for an M1919, and bulletproof armor close to five inches thick". Campbell comments that these are all parts for a tank or armoured vehicle. Snake, then received a call from someone calling himself "Prividyenie," or "Ghost" in English. Ghost thanked Snake for taking care of Volgin, much to Snake's surprise, and asked if he remembered Sokolov's Shagohod, leading Snake to conclude that the prototype weapon could be a nuclear tank. Remembering that the Shagohod could only fire a single IRBM, and couldn't possibly hit every major city in Russia from the peninsula, Ghost reminded Snake that America had already successfully developed MIRV, a single ballistic missile capable of carrying multiple nuclear warheads, and able to strike several different locations. This new nuclear weapon though, made up for the drawbacks of conventional MIRVs, by being able to launch into an enemy country and completely neutralize it all by itself, with no support required. The weapon was much smaller and more mobile than the Shagohod, reminding Snake of Granin and his Metal Gear concept. Ghost concluded that this "Metal Gear", was a small walking tank, able to launch multiple small nuclear warheads and Gene was planning to arm it with Soviet nukes. However, he assured Snake that it was still in preparation stages. He commented that a government official must have helped FOX to steal the weapon and was most likely hiding at the airport. Ghost then gave Snake his radio frequency and told him that he was counting on him to stop Metal Gear.

Python After deploying more spies to the peninsula, the group stole documents that helped to identify the location of the warhead storage facility. Campbell decided that instead of sending in a spy unit first, and with the knowledge that a transport team will arrive to pick the nukes up soon, they infiltrate the facility immediately. Upon finding the facility’s power generator, the group planted explosives to destroy it, so as to render the main elevator, used for moving the nukes from the lower floor, inoperable. The TNT, however, fails to explode, due to Python freezing the detonator. He emerged from the shadows, criticizing Snake for his recklessness, since the explosion would have been too powerful, and blocked off his only escape route in the process. Python revealed that he had survived their top secret mission in Vietnam, though his body had lost the ability to regulate its temperature. Without the suit he wore, which was filled with liquid nitrogen, his body temperature would rise uncontrollably. The CIA kept him alive so they could use him against Big Boss because they feared him, training him as an “Anti-Snake” soldier. He had been issued wetwork missions so as to keep his assassination skills sharp, which caused him to suffer from nightmares relating to every single person he had been ordered to kill. Python then cocked his rifle, and demanded that he and Snake fight.

After an intense battle, Python fell to the floor, amazed at Snake's abilities and remarking that he "won't have to take another life". He told Snake that he had followed Gene because he had promised redemption but realized that "soldiers can't find redemption in the "good of a nation" or in the "hatred of an enemy". Soldiers need heroes, for whom they would gladly risk their lives." Python asked Snake if he could bear the burden of holding his men's lives in his own hands.

Regrouping, the Snake’s unit realized that they failed to stop the transportation of the nukes, and that the only one option left was destroy Metal Gear itself. Since there were only a few places on the base that a weapon of Metal Gear’s size could be housed, plus, the fact that more people would know of its location. This reminded Snake of Ghost's words about the government official who helped sneak Metal Gear out of America. After the spy units confirmed visual confirmation of several aircraft, they determined a rough location of the Airport based on this. Snake and his sneaking unit quickly made their way inside, located the government official and interrogated him. It wasn't long before the official gave away the location of a missile silo, located east of the ravine.

Infiltrating the silo entrance, the group attempted to locate the exact location of the entrance to the silo proper. As they closed in on the entrance, an alarm was raised, and the perfect soldier, Null, was released to confront the intruders. Snake attempted to shoot him, but Null deflected the bullets with his machete. After a long fight, Null asked Snake why he still lived, since no other man had faced the perfect soldier and survived, and remarked that Snake was different. As Null screamed in pain, Snake began to realize that he had met the young soldier before, but his thoughts were cut short by the arrival of Cunningham and his men, who knocked Snake unconscious. Cunningham then ordered Null to stand down, telling him his mission was complete.

Rescue Effort

Campbell informed the men that they had lost contact with Snake, but assured them that the legendary Big Boss would not let himself be killed easily. They initiate a plan to interrogate the men at the silo entrance, Snake's last known whereabouts, and see if they can find out anything that may lead them to him. After interrogating an enemy officer, they discover that Snake was being held in the guest house.

Meanwhile, Snake himself received further interrogation by Gene and Cunningham. Gene remarked that information extracted via physical torture was unreliable, with Cunningham replying that to Snake, this pain doesn't even qualify as torture. Cunningham suggested using truth serum on him, to which Gene remarked that information extracted via truth serum is also unreliable, before questioning Cunningham's methods and asking him why he was in such a hurry. Cunningham assured Gene it was because he was working from an efficiency point of view. Gene accepted this, but under the condition he be allowed a moment to talk with Snake alone.

Gene questioned Snake on his loyalty, and asked what he was fighting for, telling him that once someone has inherited the soul of a warrior, they can never leave the battlefield. Gene went on to reveal that the whole Metal Gear hijacking was a set-up. He explained that while the Soviet Union’s planned economy had failed, and their finances in shambles, thanks to the loss of the Philosopher's Legacy, America had succeeded in deploying MIRVs in battle, and was moving to cement its military superiority through SALT. The global balance of power would soon tip heavily in America's favor, and with it, the CIA's importance would diminish. So the CIA planned on giving Metal Gear, a weapon far more advanced than any MIRV, to the Russians as a valuable trump card, continuing the age of soldiers and spies. FOX's orders from the CIA were to steal Metal Gear during transport, then pretend to defect to the Soviet Union. Snake, refused to believe it, but Gene continued, saying just as soldiers needed talented officers, men needed talented leaders, and he was created for that purpose. The Successor Project, which created Gene, was a top secret US project designed to create the perfect battlefield commander, giving him “the skills to wage war, the aptitude for strategy, the endurance to return from battle alive, and the charisma to overwhelm and master the hearts of soldiers.” The soldier they chose to use as a model leader was The Boss herself. Gene commented that he and Snake were like brothers, and told him that he was about to witness the birth of a new world.

Realizing that it would be difficult to find the guest house, Campbell sent out the spy unit to gather intel. After discovering that there was a map detailing the way to the guest house at the rail bridge, and that government officials in the town might know the way, Campbell ordered the sneaking unit to infiltrate and interrogate the men to get further info, as well as steal maps.

Later, Gene spoke on the telephone to the GRU Major, Ocelot, who informed him that negotiations with the Kremlin were a success, and that they would not interfere with his plans, having seen Metal Gear’s trajectory data. Gene thanked him, and proceeded to question who had helped him obtain the data, before shrugging it off and commenting that he had a good idea who it was: “the man with the same code-name as Null.” Gene asked Ocelot if he knew that he would be betraying his employer, and concluded the conversation by saying they would meet again one day, in a world of Gene's creation. Shortly thereafter, two soldiers charged into the room, before being cut down by Null, who was in pursuit. Null demanded to know where Snake was, since, in his eyes, he was still alive and he had therefore not completed his mission. Gene took down Null and ordered for him to be taken back to the preparation chamber. Gene was impressed: Null had his memories reset after every mission, but his battle with Snake had left such a strong impression on him that he could not forget it...

As Snake laid in his cell, Elisa persuaded the guard to leave and give her some time alone with Snake, explaining that “sometimes she longs for a strong man." Once inside, she expressed surprise that Snake was able to fight Null and survive, and gave him some food to eat. She then embraced Snake, and communicated to him telepathically, so that the guard would not hear, warning him that she was not strong enough to talk for very long. She informed him that Gene was preparing to launch Metal Gear, with Snake replying that it was too early, and asking if negotiations had broken down. Elisa responded that not even she nor Ursula could tell what was going through Gene's mind. She continued, saying she thought Gene might launch Metal Gear, no matter how the negotiations turned out. She informed Snake that they had moved Metal Gear from the harbor to the assembly plant in order to load it with nuclear warheads and that now was the perfect time to destroy it. Snake wondered why she was telling him this, to which she responded that she had a vision of him destroying Metal Gear and that he had the chance to stop a nuclear holocaust. She lets go, visibly exhausted from using her energy to communicate with Snake, just as the guard returned, asking her to wrap things up. As she left, she turned to Snake and whispered "Please, Snake... You have to believe."

After making their way to the guest house, the sneaking unit, led by Jonathan, managed to find Snake. He questioned why they would risk their own lives to save him, especially considering they didn't even know for sure if he was still alive, to which Jonathan responded that he was their Boss and they needed him, and he shouldn't forget it. Snake, his spirit obviously lifted by this, told them that he knows where Metal Gear is, and it was now time that they finished this. Jonathan assured him the area ahead was only lightly guarded, but as they advanced they were ambushed by Cunningham. Cunningham applauded Snake, telling him he led capable men, but that thanks to Ursula, he would not slip through his fingers. Cunningham questioned Snake again on the whereabouts of the Legacy, saying he knew that Snake stole the KGB's half. After Snake once again denied any knowledge of the Legacy’s whereabouts, Cunningham began to shoot Snake's men until he changed his mind, letting slip that he knew Snake had it because the Pentagon had told him so. Snake questioned his stake in the operation, but as Cunningham prepared to shoot more of the men, a truck driven by Elisa barged in, ramming into Cunningham's hover-platform and sending him flying. Snake, gathering his wounded comrades climbed aboard, and Elisa sped off.

Elisa

After returning to the group’s camp, Elisa asked Snake to follow her, as the night would make finding the assembly plant easier for them, as its lights would tell them exactly where it is. As they walked through the woods, Snake asked Elisa why she decided to betray Gene and help him. She told him that she was grateful for what Gene had done for her and Ursula. In East Germany when they were younger they were treated like guinea pigs, but he saved them. She goes on to comment that the Communists and Americans were the same in wanting to unlock the secret of their ESP. But in the end, she betrayed him because of the nukes: “No one should be allowed to use nuclear warheads.” Elisa and Ursula's parents were killed in the accident at the Kyshtym facility, and it was the after effects of this that gave them their ESP. Elisa suffered from nightmares about the incident, seeing the ashes of death raining around her. Snake consoled her, saying that he had been exposed too, at Bikini Atoll. After Elisa said that she knew, he asked her if that was why she helped him. She said that that was probably the reason, but she also thought that he would make a great father someday, and she was unable to have children of her own. Snake told her that he would never be a father.

They then approached the perimeter of the assembly plant, and Snake asked her if it was where they were storing Metal Gear. She says that she believes so, but Snake senses that something isn't right as personnel were still working late into the night. Since Null was still undergoing readjustments, with Elisa gone he wouldn't be deployed for another few days, thus making it the perfect chance to investigate. Snake felt that the only person he had to worry about was Cunningham, but Elisa revealed that Gene was more of a threat, as she revealed that the Successor Project was also designed to create a battle commander capable of commanding the Perfect Soldier. She had never actually seen Gene fight, but she suspected that he had even faster reflexes than Null, not to mention that his very battle technique was patterned after the Boss herself. After revealing her fear of Gene, Elisa explains that her sister foresaw that Snake would plunge the world into fear, but that she saw him destroying Metal Gear. It was the one time their visions weren't one and the same, hence why she believed in Snake.

RAXA After arriving back at camp, Campbell delivered the news to the group that they had finally discovered the location of Metal Gear. It was currently being loaded with nuclear warheads at the assembly plant, and so was extremely vulnerable. They proceeded to infiltrate the plant and entered Metal Gear's deployment station. Elisa told Snake that they needed to hurry up and to start planting the explosives. Unfortunately, Gene's army discovered them before they got the chance to do so. The guards proceeded to apprehend Snake, but Metal Gear suddenly became active and fired on Gene's position. While successfully killing several of Gene's men, it failed to actually hit Gene himself, who seemed to avoid the bullets without appearing to move. The pilot revealed himself to be Colonel Skowronski, who was amazed at the power of Metal Gear and attempted to wipe out all the "turncoats at the base" along with Gene. However, Metal Gear stopped firing unexpectedly before he could even aim at Gene again. Snake used this distraction to his advantage, holding Gene at gunpoint and telling him to order his men to drop their weapons. Gene, however, decided to play his trump card and ordered Ursula to awaken. Elisa then begins to struggle with something, shouting at Snake to shoot her before Ursula awakens. Confused, Snake hesitated and Ursula was able to “awaken”, revealing herself to be Elisa’s split personality. Ursula told Snake that she would kill him before he could spawn his "accursed snake children" and effortlessly pushed him aside using her psychokinesis. Gene explained that her split personality was a side effect of her powers being artificially augmented, and that a greater percentage of their overall powers went to Ursula, at the expense of her emotions. He also revealed that she could more than make up for Metal Gear's shortcomings, by enhancing its movements beyond its full potential, causing it to behave in an animal-like manner. Skowronski was then thrown from Metal Gear, while Ursula descended into the cockpit, preparing to attack Snake and his unit. Gaining advice from Ghost over the radio, Snake attacked the weak points in its legs with the RPG-3 and TNT. Toppling over, Ursula continued to attack Snake, causing Metal Gear to crawl towards Snake with its now-exposed missile pods firing on him. Avoiding the incoming missiles, Snake used the RPG to destroy the pods, desperately warning Elisa to get clear, but Metal Gear exploded with Elisa/Ursula still inside, apparently killing her.

While Snake mourned over what happened, Gene’s men gave up the will to fight, since without Metal Gear, they could never build their nation. Gene then congratulated Snake on his defeat of Metal Gear RAXA with Ursula at its helm, realizing now why Snake had caught Ocelot's eye. Snake demanded to know what Ocelot had to do with the situation, but Gene simply laughed and told Snake that he was a fascinating man. Snake ordered him to surrender, since he could no longer carry out a nuclear attack. He was then contacted by Ghost, who told Snake that it was not over, as the Metal Gear that he had destroyed wasn't the ballistic launch Metal Gear, it was merely a test model for performance evaluation. Ghost then stepped into the hangar in person and revealed his true identity: Nikolai Stephanovich Sokolov.

After the initial shock of seeing him alive, Snake then realized that Sokolov would naturally know about Granin's Metal Gear, seeing as he originally designed the Shagohod. Sokolov explained that he was still grateful to Gene for rescuing him from a Russian prison camp, and reuniting him with his family for a short time. However, despite his gratitude, he simply could not bear to see his creation, Metal Gear, be launched against his native country. Gene then reminded him that he was a Soviet rocket scientist who defected to the United States, and that one day the United States would, indeed use Metal Gear against the Soviet Union. As Sokolov stood there speechless, helicopters overhead were seen transporting a large machine. Snake realized that it was the real Metal Gear, and that Ursula had bought plenty of time for it to be taken away. Snake once again demanded for Gene to stop, with Gene telling him to pull the trigger, but he warned Snake that the future may not be the one he wanted to face after inheriting the title of Boss. Gene then told everyone that the Cold War would soon end, but that did not mean that peace would come afterwards. He mentioned that as the hate died down, and the gap between rich and poor widened, nuclear weapons would spread across the world, hinting that today's ally could be tomorrow's enemy or even worse, people in the same countries would kill each other. He asked if any of them wouldn't end up pointing their rifles tomorrow at their neighbors, comrades, or even families. Snake yelled for Gene to stop, but he continued to invoke fear and paranoia within the soldiers minds, using his specially-enhanced voice. Gene claimed that an enemy was standing right in their midst, and began asking which of them it was. He then says he has found the "enemy," throwing a dagger at one of Snake's men, and causing him to begin shooting. Suddenly, a riot broke out between both Gene’s and Snake’s soldiers, who start firing at one another. Snake desperately tried ordering them to cease fire, but it was no use, and he ended up being grazed on the arm. Gene then began to leave, having no more use for the base, since Metal Gear's launch was nearly ready. Snake cursed him for killing his own men, though Gene replied that they are perfectly capable of doing it themselves. Revealing his disgust towards humanity by claiming them to be foolish, fragile, and violent creatures, Gene told Snake to watch what humanity truly was. Suddenly, Jonathan dived in front of Snake, as bullets are about to hit him, and was himself hit in the chest and head. As Gene departed for his helicopter, and Jonathan laid dying in his arms, Snake lifts his head up to the sky and yells out in anguish, surrounded by the bodies of fallen comrades,

After returning to the encampment to report the bad news, Snake and Campbell decided that they couldn't afford any more setbacks, and set up a spy unit at the silo entrance, to discover a way into the silo complex. Snake was still affected by the death of Jonathan, as well as the possible deaths of most of his squad. Half a day later, their spies managed to procure technical documents detailing the structural layout of the launch silo, specifically the gate entrance. The gate was impenetrable, so it couldn't be breached via normal means. However, the lock system of the gate used an electromagnet, so cutting the power, would allow the gate to be unlocked manually until the auxiliary power came on. They therefore needed to sabotage the power substation before they could infiltrate the underground complex. After discovering the substation’s location, to the south of the ravine, Snake immediately headed for the facility. After realizing they don't have enough explosives to destroy the entire complex, the group decided they should destroy the switchboard, but they would be unable to make it back to the launch silo within five minutes. The group got their technical unit to build a time bomb and Snake returned to the substation. After placing the bomb on the switchboard, he attempted to leave, but on his way he encountered a grizzly site of several soldiers’ corpses.

The Frank Hunter

Snake heard a slicing sound and a man screaming, and he then realized that Null was present. The soldiers were confused as to why the Perfect Soldier had been deployed, since he was still supposed to be undergoing readjustment. After killing several more of them, Null demanded to know where Snake was. He then immediately sensed him behind him, and asked why he was still alive. Null told Snake that he used to get dreams about his allies saving him, but when he woke up, he had nothing, only the corpses of the men he'd killed lying in front of him. He continued on, saying that everybody dies, either by crime, disease, accidents, or war, even if he isn’t the one to kill them. But he was confused as to why Snake still lived, and what he hoped to accomplish by living. Null suddenly made to attack, but Snake is able to block his attack. Finally realizing who he was fighting, Snake told Null that he knew who he was, and that they had met back in Mozambique, four years ago. Null had been a child soldier fighting in a guerilla group in the struggle for independence. There, he had killed several government soldiers with a single knife, as he threw them off guard with the innocent frankness of a young boy, and then preyed on them with the cold cruelty of a hunter. Because the boy spoke a little German, both comrades and enemies referred to him as Frank Jaeger, “The Frank Hunter.” As Null began to remember this name, Snake tried to convince him not to fight with FOX, and that his allies could be found somewhere else. Null refused, however, as he was The Perfect Soldier, and where he existed, no other soldiers existed, and therefore didn't need a name. He then declared himself to be Null, and that after he killed Snake, he could go back to being Null. He then fought Snake, and after an intense duel, Snake manages to defeat him. Null, now reasserting his identity of Frank Jaeger, kneeled down to Snake, he then said that he remembered now who he was, and that even back then, Snake had managed to stop him. He took off his mask revealing his face for the first time to Snake. He told him how adults had raised him to be a tool of war, but that Snake had defeated him and watched over him. Snake then apologized for what happened as he thought he had placed him in a safe place when he took him to a rehab center. He had no idea that he would be subjected to The Perfect Soldier project, and immediately held the Philosophers responsible. Frank Jaeger then forgave Snake, as he helped to fill the void in him, and that he would always be there to save him. Snake then helped him back to the group’s base camp, as they were now going to take the power grid offline.

Cunningham

After heading to the launch silo, and reaching the entrance, they detonate the bomb at the power station, giving Snake five minutes to reach the gate within. He successfully accessed the gate in time and infiltrated the complex, eventually reaching a freight elevator leading down to the silo. However, after beginning his descent, Cunningham appears atop his flying platform. Surprisingly, he wasn't waiting there to attack him or even interrogate him. He hadn’t thought that Snake would make it this far, and that "he" had been right about Snake. Snake didn't know who he was referring to, then Cunningham told him that he had no reason to fight anymore as his mission was already complete. Snake was naturally confused as to what he was talking about, so Cunningham explained that he didn't answer to Gene, nor the CIA, but actually the U.S. Department of Defense. He then asked Snake if he had noticed that the CIA and the Pentagon weren't on the best of terms. Apparently, the Pentagon brass had become worried of the CIA's growing influence in military affairs due to events such as the Bay of Pigs Invasion in 1961 and the covert operations in North Vietnam, and even the creation of Metal Gear. They had arranged for Gene to steal Metal Gear and launch it into Russia so that the CIA's reputation would be tarnished and the United States military would take charge again. Snake called Cunningham out on the madness of the plan, as it would end up starting a nuclear war. Cunningham then revealed that as far as the world was concerned, Gene was a renegade, and the fundamental design of Metal Gear as well as it's missiles were Soviet made, so they wouldn't even think of blaming Washington, and besides which, there would be no evidence left behind anyway. He then reveals that he has a Soviet-made Davy Crockett missile launcher with him, which he intended to use against the missile base as soon as Gene launched Metal Gear. When Snake asked him about the fates of the other soldiers, Cunningham laughed and replied that he didn't care what happened, since they were their enemies. He added that Snake was different though, and that he had followed the “script” of the mission down to the letter. Apparently, the real reason he had been sent to the San Hieronymo Peninsula was because “they” knew that the legendary Big Boss would throw a wrench into Gene's plan: he would sneak into the missile base alone, recruit the rebels to his side, and force Gene to launch Metal Gear. The entire mission was part of the Pentagon's plan and since they didn't want Snake interfering further, Cunningham attempted to convince Snake head up to the heliport at the top of the base and get onto a waiting chopper. After Metal Gear was launched as planned, Snake would be sent back to the United States, and be hailed as a hero yet again, though it wouldn't be the CIA congratulating him this time.

Having heard enough, Snake then pointed his pistol at Cunningham, who then enquired if Snake was still blinded by his loyalty to the CIA. He then asked him what they had ever done for the FOX unit, citing the fact that they were sent on brutal missions, and when he lost his leg, he was confined to a desk job. They had also sent the Boss, the Mother of Special Forces, to a foreign land to die. With Snake refusing to lower his gun, Cunningham then asked if he was doing it for the Russian soldiers on the Peninsula, and remarked that it was pathetic. He said that he wouldn't let him through and that he should go back. Snake replied that he simply could not allow the use Metal Gear, and that he was doing this out of loyalty to himself, refusing to live his life the way The Boss did. Cunningham laughed at this and then declared Snake to be a real traitor. After a difficult fight with Cunningham. Snake was able to significantly damage Cunningham's flying platform. Cunningham laments Snake's decision, since if he did what Cunningham was told, both he and Snake would receive the highest awards that any soldier could dream of. However, he declared that he wouldn’t die alone, and that he will take Snake with him. Cunningham readies the Davy-Crockett and Snake yelled for him to stop. Cunningham laughed insanely, but before he could launch the warhead, the flying platform he is on exploded, and the Davy-Crockett Launcher flew from his hands. The platform fell and was obliterated, along with Cunningham.

Gene

Campbell reminded Snake that the preparations on Metal Gear were almost complete, and that he should stop the launch by any means necessary. Snake managed to reach the silo’s control room, where he found Gene, standing among a number of corpses. Snake realized that the corpses were those of the Metal Gear engineers and accused Gene of having murdered them. However, Gene denied any involvement in their deaths, as they had chosen to commit suicide due to their crimes. Snake then asked if this "crime" was the fact that this was all a Pentagon conspiracy, with Gene remarking that Cunningham was a poor fool for dying without realizing that he was just a puppet. Snake asked if it was in fact Gene who was the puppet, and pointed out that the Pentagon was trying to get rid of the CIA. Gene revealed that he already knew everything that would transpire, including the Pentagon's plans and that Cunningham would betray him. He only allowed it to happen so that he could utilize his real plan. He wouldn't be launching Metal Gear into the Soviet Union, and he speculated that the Pentagon was prepared for the possibility that Cunningham would fail to destroy the evidence, and would be meeting with the Red Army as they spoke. Because of this, even if he launched Metal Gear into the Soviet Union, it wouldn't trigger a war. He then revealed that he was actually going to launch Metal Gear at Virginia, USA, home to both the CIA headquarters at Langley, and the Pentagon: the twin lairs of the Philosophers. Snake was horrified at this, with Gene explaining that chaos would spread at an unprecedented scale, and that the worst case scenario would result in America ceasing to exist as a nation. The current world order would crumble and the fact that Metal Gear would be launched from a Soviet missile base would stir up international controversy, resulting in the Warsaw Pact crumbling and possibly facing armed conflict with NATO.

Snake demanded to know why Gene would do this. Gene replied that he wanted to free the world from the Philosophers influence, and create a new world order of his own design. His goal for making a nation for mercenaries may be real, but it wasn't to be on the San Hieronymo Peninsula. In fact, this nation would be an organization of shadows, lurking deep underground and intervening in conflicts all over the world. He intended to create what the Philosophers could not create with a superior breed of soldier, and that this organization would be the true "Peninsula of the Dead.” This organization would be known as "Army's Heaven". Gene explained that he would not allow the world to be a playground for abstract national interests or petty political gambits. He intended to use superior force of arms to enforce a superior force of will, thus making the world whole again, as this is his calling, as The Successor. Disgusted by this, Snake tells him that he was nothing more than a dictator, using fear to keep his soldiers in line, deceives his allies with words, exploiting those who looked up to him as a mentor and then throwing them away. He also told Gene that the nation he was building was no heaven for soldiers, and that the place they were looking for was outside Gene's "Heaven". Gene then told Snake that this was their calling, and it was all part of a greater mission. “The individual wills of individual soldiers are meaningless.” He told Snake that those who had no calling must be given one by those who did, and they must follow the teachings of a superior will, devoting themselves to a higher cause. They must pour their lives into the cause, just as The Boss once did, with Snake angrily remarking that Gene was full of himself and was not worthy to speak The Boss’s name. Deducing that Snake never knew the whole truth of The Boss's sacrifice, Gene told him that during the Virtuous Mission, Volgin did not destroy the Sokolov research facility of his own free will, but that it had actually been the work of America, and a single deviously cunning strategist. Snake demanded to know who set it up, but was ignored by Gene, who stated that The Boss had sacrificed herself for someone's will, a noble act. Saying that Snake does not need to know who was behind it, Gene said that the only thing he needed was a calling, and that he should join Gene, and receive it. Snake refused, with Gene remarking that he was a true soldier after all, and that it would be a shame that they wouldn't meet eye-to-eye.

Telling Snake that the time for talk was over, Gene proceeded to commence Metal Gear’s launch, but as he pressed the button, the entire console mysteriously exploded. Gene was surprised at this, until he saw Elisa/Ursula. She smashed her way through the window, into the control room, with Gene demanding for “Ursula” to stay out of his way. Ursula/Elisa then said that nuclear weapons should never be used, that they are terrible weapons, which cause the earth itself to suffer. She stated that she knew “their pain, their suffering, their cries, their hatred.” Snake wondered if it was Ursula or Elisa who was speaking. Gene then threw a knife at Ursula/Elisa, which she effortlessly deflected. Knowing that she had read his thoughts, Gene realized that he had let his mental defences down when he believed she had died. However, she could not keep track of body, and Gene charged towards Ursula/Elisa at impossible speed, stabbing her. Gene then left with Snake yelling for him to come back. Snake cradled the dying Ursula/Elisa in his arms, who tried to tell Snake that the trajectory data had already been input, and that there was a backup launch control in a nearby room. She revealed to Snake that their visions were one and the same, that Snake would destroy Metal Gear, and that he would build another in its place. One of his children, Les Enfants Terribles, would bring the world to ruin and that another would save it. Snake tried to ask her what she meant, but she fell silent, and he shouted her name. Realizing she had passed away, he then stood up and pursued Gene.

Snake rushed to the backup control room where Gene informed him that Metal Gear had already entered launch mode. The trajectory calculations and the target locations had already been set, and that no one could stop it, not even Snake should he defeat Gene. Knowing that Snake wouldn’t give up without a fight, he revealed that he had his own reasons to fight Snake, which was to find out who the true successor to The Boss was. They then fought, with Snake constantly being plagued by Gene's telepathy, quoting the Boss at one point, and trying to cast doubt on Snake. Regardless, after an intense duel, Snake managed to defeat Gene. Gene expressed disbelief that a product of The Successor Project such as himself could be defeated by a man of flesh and blood like Snake. He then admitted that Snake was the true successor after all, and that perhaps a story he had heard, concerning “soldier genes,” was true after all. Snake then asked him how to stop the launch, but Gene replied that there was no way to prevent it now. He told Snake to escape, and handed him a microfilm, saying that it contained information on the equipment, personnel, and funding for Army's Heaven, gathered in secret. Snake then asked Gene why he was giving it to him, with Gene replying that he did it because they were the same. He told Snake that he would be glad to have them someday, and mentioned that it was their fate, telling him to go find his own calling. Gene then died.

ICBMG

Metal Gear was primed to launch and the silo opened up. Sokolov called Snake, telling him that the control panel had been locked out and that the countdown had began. He mentioned that the rocket booster didn't have a post-ignition fuel control system, meaning that he couldn't stop Metal Gear after it was launched. Snake told Sokolov that he didn't care if he had to blow up the entire base, as long as it stopped the nuke. Sokolov revealed that he may have a chance at stopping the strike if he dismantled the Metal Gear unit itself, atop the rocket. He explained that Metal Gear was not the same as a nuclear missile, as it would be jettisoned from the booster at 3000 feet and parachute down to the ground, where it would release its payload of miniature nuclear missiles. By destroying Metal Gear before it launches, the nuclear strike could be averted, if not the actual launch. However, the designers had anticipated that such a possibility would occur, so they gave it armor thicker than a tank’s. He also advised that Snake shouldn't try to destroy the rocket, lest he risk the destruction of the entire silo. Snake then raced out of the control room onto the launch pad, and used an RPG launcher to damage it. Though the RPG landed a direct hit, Metal Gear seemed to be unaffected. Suddenly, automatic weapons were fired at the Metal Gear with the bullets bouncing off for the most part. Snake looked up at the catwalks to see his fellow resistance members firing their weapons madly at Metal Gear. Snake yelled that their weapons wouldn't work and that they should get out of there before they got caught up in the ignition blast and killed. Telling Snake that he had risked his life to save Russia, they replied that they were repaying him the favor by helping to save America, and for giving them a real reason to fight. Snake agreed and launched another RPG at Metal Gear just as it gained liftoff, knocking Snake off his feet. Sokolov attempted to contact Snake that Metal Gear was in launch and that it was too late. However, as the rocket reached its second launch phase, it became apparent that the blows that Snake and his comrades had inflicted had caused structural damage, and the Metal Gear exploded upon reentry into the atmosphere. Sokolov attempted to contact Snake to tell him that Metal Gear had successfully been destroyed, and the pieces were falling back down to Earth, as well as the fact that the launch tubes had been sealed shut. However, he receives no answer.

Meanwhile, in Langley, the Director of Central Intelligence and two body guards proceeded down a hallway leading to a secret bunker. On the way, they encountered an unknown man, who expressed amazement that they would have a bunker right under the CIA, and that if FOX was still around, he would not have been able to sneak down there. He told the DCI that he had been sent to meet him, and introduced himself as ADAM. The DCI remembered him as the triple-agent for the Philosophers, and realized that he was Ocelot. Ocelot then told him that Metal Gear had already entered launch mode, and that the nuclear warheads would be arriving in thirty minutes. The DCI revealed that he was aware of this, and in fact was already on his way to the shelter, but that he couldn't leave behind certain documents, related to the Philosophers. The DCI mentioned that it contained a list of members, along with data and locations of portions of the Philosophers’ Legacy stashed around the world. He added that even if America was destroyed, as long as he had them, then the Philosophers would be reborn. After hearing this Ocelot then shocked the DCI by shooting his accompanying men, and wondered if Ocelot planned to betray the Philosophers. Ocelot replies that he actually plans to end them, and that he would take back what they “stole” from them, and “carry on the spirit of the true patriot.” Ocelot explained that it was part of a greater plan to make the world that The Boss envisioned a reality. He revealed that he had come to retrieve the other half of the Legacy, before shooting the DCI himself.

Comradery

Later, Snake disembarked from a plane that had landed back in the US, having survived Metal Gear’s launch. He was greeted by Sigint, Para-Medic, and Major Zero where he received some official looking documents. He then looked beyond Major Zero and saw his comrades shuffling off another plane. They salute Snake, and he returned the gesture. Afterwards, he spoke with Roy Campbell over the phone, who was currently in hospital, and told him that he was almost fully recovered. Campbell informed him that Frank, the child soldier from Mozambique, was also doing fine, but that he was a mess, both physically and mentally. He also explained that after he was released, he was not sure what he should do, and that he may never be able to go back to leading a normal life. Snake told him that the whole incident was covered up, that he had actually been deployed to take down a soviet missile base, since it would be impossible to reveal to the public that the United States had come close to suffering a nuclear attack. Campbell told Snake not to feel so beat up about it, as he had done his country a great service. Snake then admitted that he didn’t feel truly alive unless he was in battle, but that he needed to find a reason to fight. He needed to pass down what had been handed down to him. Campbell then wished him luck, and hoped that they would meet again someday. Afterwards, the documents Snake received earlier are revealed to contain official orders relating to the establishment of Unit FOXHOUND.

Meanwhile, Ocelot received a call from a mysterious man who he seemed to recognize. Apparently, this man was the one who fed Ocelot information. When asked how the DCI's death would be handled, Ocelot stated that it should pass as suicide, due to him feeling responsible for the theft of Metal Gear. He also mentioned that there would be a major shake-up on the seventh floor of Langley soon and that everything was going according to what he had planned. When asked about how the DCI reacted, Ocelot answered that when he saw the trajectory data, he brought the documents straight to him. He then agreed that the DCI should have known that Gene was serious about launching the nukes, and that Gene did well as their insurance plan. He then asked if his getting the legacy was part of a script as well and that only “he” would use Gene and FOX like that. Ocelot told him that he wouldn’t be using him anymore. The mysterious man then mentioned about the battle data he had received from The Perfect Soldier, and mentioned to Ocelot about soldier genes that were related to it. Ocelot then became interested in helping him with his project, though under the condition that they recruit Snake, so they can become The Patriots.